Abstract
Next-generation sequencing is increasingly being used to study samples composed of mixtures of organisms, such as in clinical applications where the presence of a pathogen at very low abundance may be highly important. We present an analytical method (SIANN: Strain Identification by Alignment to Near Neighbors) specifically designed to rapidly detect a set of target organisms in mixed samples that achieves a high degree of species- and strain-specificity by aligning short sequence reads to the genomes of near neighbor organisms, as well as that of the target. Empirical benchmarking alongside the current state-of-the-art methods shows an extremely high Positive Predictive Value, even at very low abundances of the target organism in a mixed sample. SIANN is available as an Illumina BaseSpace app, as well as through Signature Science, LLC. SIANN results are presented in a streamlined report designed to be comprehensible to the non-specialist user, providing a powerful tool for rapid species detection in a mixed sample. By focusing on a set of (customizable) target organisms and their near neighbors, SIANN can operate quickly and with low computational requirements while delivering highly accurate results.
Introduction
There are many different methods that characterize the mixture of organisms present within a metagenomic dataset. Such datasets are generated when a complex environmental sample is processed by a “next-generation” high-throughput genome sequencing protocol, and they consist of large numbers of short nucleotide sequences. Each sequence represents a small fragment of a randomly selected genome from the very large collection of genomes present in the source sample. Those sequences indicate the presence of one organism or another according to their similarity to a set of known reference genomes. While a given sequence may be unique to one species, it also may be found in diverse organisms across the tree of life. Therefore, one analytical challenge (among many) is to take that collection of sequences (likely numbering in the millions) and accurately determine what species are present in the sample. Here we describe a novel method (SIANN: Strain Identification by Alignment to Near Neighbors) that is specifically designed to rapidly detect a set of targeted organisms from a metagenomic dataset by aligning reads to genomic regions that are unique at the strain or species level.
The analytical question motivating a particular piece of metagenomic bioinformatic analysis may vary widely by user and sample type (Segata, et al., 2013). For example, the function of the human gut microbiome may depend on the relative abundance of hundreds of species of bacteria and the types of metabolic genes they contain (Wu, et al., 2011; Schloissnig, et al., 2013). In contrast, the clinical treatment of a patient may depend on whether or not a particular virus, or a consortium of co-infecting pathogens, is/are detected in their blood. It is this second class of presence/absence questions that SIANN is designed to address. SIANN is appropriate for situations in which a user wants to know whether a particular organism or set of organisms is present in a sample, but isn’t interested in the functions encoded in their genomes, the relative abundance of each organism, or any other more in-depth analysis.
Methods
Approach
Metagenomic classification methods are based on a wide variety of theoretical underpinnings. The basic varieties include alignment of reads to various nucleotide databases or exact matching to nucleotide or protein signature sequences (or kmers). A representative set of recent methods are described in Table 1 (also see Bazinet & Cummings 2012).
Overall, these methods are designed to either classify individual reads to, and/or predict the total abundance of, clades (e.g. genus or species) across the entire tree of life. They generally require reference databases that are very large and/or require a large amount of processing to generate. The gap SIANN is designed to fill is when the entire tree of life is irrelevant, and only predefined subsets of organisms need to be detected. For an underlying method we chose read alignment to diagnostic genomic regions because the algorithms for read alignment are highly parallelizable and have been optimized heavily by the community at large (the current implementation of SIANN uses bowtie2 [Langmead & Salzberg, 2012] for the alignment function, but can be adapted to any alignment algorithm). This approach is distinct from using clade-specific marker genes (Segata, et al., 2012) because unique regions that are larger, smaller, or outside of genes can also be used. Furthermore, this approach supports the rapid construction of custom databases using reference genome sets that require only minimal user-supplied structure.
To understand the principle at work, consider a set of reads that have been aligned to the genomes of several strains belonging to two species. Some regions of those genomes are species-specific, some are strain-specific, and some are shared (Figure 1a). When a set of reads is aligned to those genomes such that each read is placed in as many locations as it has a match (at a reasonably stringent threshold), visual inspection of the distribution of reads yields an intuitive understanding of the true source organism as Species I/Strain B (Figure 1b). If Strain B were not present in the reference database, it would still be clear that the organism was an unknown strain of Species I.
The unique identification of a species or strain is quantified by the proportion of the genome that is determined to be species- or strain-specific (defined as reads that are aligned to regions that are species- or strain-specific). Each species and strain is then assigned a numerical measure of the proportion that is covered by these diagnostic reads, and that proportional measure is compared to the ideal case, where sequences from a single organism (generated in silico) are aligned against the database in an identical manner. After that normalization factor is applied, the resulting score indicates whether the source sample contained any of the organisms in the reference database. The analysis is conducted independently on both the species and the strain level, so that if the true strain is not present in the database, the species of origin will still be identified. While many methods consider the complete taxonomic tree and assign reads to the least common ancestor, SIANN considers only two taxonomic levels: species and strain, throwing out anything that is not unique at one of those levels and thus obviating many of the confounding factors introduced by manually curated taxonomies.
The example shown in Figure 1b indicates that species-specific reads are identified as reads that align to one species (Species I, in that case) but not the other. If Species II were not present in the example shown in Figure 1b, a much larger number of reads would be assigned as “species-specific,” when in fact those regions are shared with other species. Therefore, the ability of this method to identify strain- and species-specific sequences is a direct function of the inclusion of near neighbors in the reference database. This characteristic is shared among many classification algorithms, but it is of particular note for this method when users have an opportunity to construct their own database. In order to detect a target species with a high degree of specificity (reducing false positives), it is necessary to include other related species in the reference database. Only by parallel alignment to those near neighbors can the redundant sequences be separated from the species-specific ones. For example, in order to detect Bacillus anthracis in a sample, it would be necessary to include other species of Bacilli in the reference database so that the presence of B. cereus or B. thuringiensis in a sample does not lead to a false call for B. anthracis.
The nomenclature of genus, species, and strain is potentially problematic because it does not correspond to a consistent degree of evolutionary distance or genomic distinctiveness. The ability to distinguish two organisms by any method using genomic sequence data is proportional to the amount of each genome that is shared or unique. One might assume that any two organisms of the same species will have a relatively predictable amount of shared genomic identity. However, some pairs of organisms from the same species may have less in common than other pairs of organisms from different species or even genera. This ambiguity impacts SIANN in two ways. If two organisms have very little genomic sequence to distinguish them, the sensitivity of SIANN to detect either one will diminish (the rate of false negatives will increase as the likelihood of sequencing unique regions decreases). Conversely, if an organism is extremely dissimilar to the near neighbors selected for the database, the specificity with which SIANN detects that organism will decline (the rate of false positives will increase as the number of related genomes available in the database decreases). For example, if a database contained only E. coli and B.anthracis, a sample containing B. cereus would be misidentified as contraining B. anthracis. In the intended use case, a database targeting B. anthracis would contain B. cereus and a number of other near neighbors to prevent that kind of misidentification. It would be convenient to say that an ideal database can be made by calculating the ideal genetic distance between all references and then finding an ideal set of organisms to make up that database, but the behavior of any database will be governed by the particular genomes of the organisms it encounters in the wild. Because not all organisms evolve in the same manner (differences in mutation rate, horizontal gene transfer, recombination, etc), the suitability of a database and method to detect a given organism can only be determined by thorough validation and benchmarking, as well as updating the reference database as needed. Users of SIANN may construct their own custom databases to include newly identified genomes or specific subsets of genomes that best suit their research interests.
Steps to construct a custom database:
Select a set of target organisms
Gather a set of genome sequences for those target organisms as well as a matched set of near neighbors
Using those reference genome sequences as an input, SIANN will:
Construct a reference index for alignment
Simulate a set of reads from each genome
Align each of those simulated read sets to all of the reference genomes
Calculate the proportion of each reference genome that is strain- or species-specific
[If two organisms do not have a minimal amount of unique sequences that exceeds the rate of sequencing error, SIANN asks that all but one of those organisms are removed from the database to eliminate redundancy. Note that the user can provide a single representative genome with multiple strain names so that the redundant strain names are not lost.]
The files contained within each SIANN database are a compressed genomic index and a list containing the proportion of each reference genome that was found to be strain- or species-specific during database construction.
To run SIANN:
Select a pre-made SIANN database and a set of sequences to be analyzed, and
SIANN will:
Align each of the reads against the reference genomes
Calculate the proportion of each reference genome that is strain- or species-specific within those reads
Compare that proportion to the simulated ideal case generated during database creation
Calculate the probability that the given results could be generated by random chance
Report the normalized proportion and non-parametric statistic of likelihood for each strain and species in the reference database. The normalized proportion of the genome covered by strain- or species- specific reads is the primary statistic reported by this tool.
Benchmarking
The performance of SIANN (version 1.6) was tested in comparison to the following state-of-the-art metagenomic classification programs: LMAT (version 1.2), MetaPhlAn (version 1.7.7), and Kraken (version 0.9.1b). All of the programs in Table 1 were investigated for this effort, and three were chosen based on their ability to run on our high-performance computing cluster with an execution time and memory requirement that would be suitable to a clinical lab. Each program was run on a set of 600 simulated datasets generated by MetaSim (Richter, et al., 2008). Each dataset consisted of 15,000,000 reads (100bp single-ended) with Illumina-simulated error (fourth-degree polynomial) (Korbel, et al., 2009). The 600 datasets were broken into 12 sets of 50 replicates. Each of the 12 sets contained organisms at different levels of abundance as shown in Table 2. Organisms were specifically chosen in pairs so that the ability to distinguish these near neighbors could be determined. The abundances were staggered at 4-fold intervals so that a wide range could be evaluated. All known species of near neighbors for each of the 12 target organisms were included in the reference database used by SIANN for this benchmarking (“Target Pathogen Database”) and are shown in Appendix 1.
Each program outputs a distinct measure. Kraken and LMAT both count the reads assigned to each taxon, MetaPhlAn calculates the abundance, and SIANN outputs a measure of the proportion of diagnostic genomic regions present. To put these measures on an even footing, we empirically calculated the false positive rate for each method over all 600 samples, at each possible measure of output. Because each dataset is made up of known organisms, any result can be classified as true or false. Therefore, for any possible result (say, 513 reads classified by LMAT or 1.6% abundance assigned by MetaPhlAn), one can calculate the proportion of calls with at least the same amount of support that were correct (True Positives/[True Positives + False Positives]), over all of the 600 datasets. That measure is commonly given as Positive Predictive Value (PPV). For each program, the results can be translated from the raw value into a PPV that is based on this empirical measure of error. The key item of interest is the PPV value for the results that we know to be true positives, the defined spike organisms. Another way of describing this approach is to say that the results of each program have been normalized to the false positive error rate that was empirically observed. If another set of samples were generated, the PPV vs. raw value curve (Figure 2) would likely fall differently, but in this case it gives us a means of comparing a diverse set of methods against the same ground truth. If method 1 detects an organism with a higher PPV than method 2 does, it means that method 1 has fewer false positives in the range that it reports true positives, which is the definition of utility in this setting.
For each method, PPV was calculated as a function of raw output value. Briefly, this was done by compiling the output for all 600 samples, labeling each result as false or true based on the sample set that it came from, and then calculating (at each possible value of output) what the proportion of TP/[TP + FP] was for results with at least that level of raw output. Some simplification steps were taken, such as focusing on the species-level assignments (for comparison with methods that do not perform strain assignment), and only taking the top hit for each species from each dataset. Custom R and BASH scripts were used for the data compilation and analysis.
Results
The relationship of raw output value to PPV is shown for each of the four methods in Figure 2. The point at which PPV is very close to 1 (where 95% of results are true positives) is ∼41,000 reads for Kraken, ∼2,800 reads for LMAT, ∼38% abundance for MetaPhlAn, and 0.21 for SIANN. For SIANN this means that having 38% of the species-unique genome covered by reads resulted in the vast majority of calls being accurate.
For read-assignment methods (such as LMAT and Kraken), manual inspection of the results may yield a different understanding of confidence than is presented here, or in any automated analysis. For example, while each read that is assigned by LMAT and Kraken fall above a certain cutoff for species-specificity, some individual reads may be much more specific than others. One could identify a read that aligns to a single species of bacteria with 100% accuracy over its 300bp length, with the next closest match being only 90% similar. It is extremely unlikely that a 300bp exact match would arise due to random chance, and so the user could say with confidence that the organism of interest is found within the sequence data (not considering contamination, horizontal gene transfer, etc). However, such an approach is not currently implemented in an automated method, and many of the steps needed to make that assertion are performed manually by a domain expert, including alignment to near neighbors and ensuring that the read does not fall within a transposon, plasmid, etc. Therefore, while one could say that a single read is all that is needed to state with high PPV that an organism is present, the amount of reads assigned in an automated manner needed to achieve that level of PPV will number in the thousands (Fig 2).
The next phase of benchmarking was to determine how many raw input reads were needed to achieve the threshold for high PPV. To demonstrate this we plotted the known abundance of each spike organism against the PPV value generated by each method (Figure 3). Each point (an organism at a known level of abundance) is comprised of a maximum of 50 replicates, where the diameter of each point increases with an increasing number of replicates. For demonstration purposes we are showing two pairs of bacteria and three viruses. Recall that for each of the pairs of bacteria (and the two poxviruses) any sample containing one did not contain the other (as shown in Table 1). The empty boxes result from the organisms not being called at any abundance. For MetaPhlAn, that is a result of no viruses being included in the version of the reference database available for this analysis. Kraken assigned no reads to Hanta virus because viral RNA genomes were not included in this version of the reference database (personal communication with D. Wood). This emphasizes the point that a) the ability to create custom databases targeting organisms of interest can be valuable, and b) the performance of any method must be benchmarked against each potential target of interest.
All methods were able identify the bulk of organisms in their databases at high abundances (75% and 18%, Figure 3), however performance varied considerably at lower abundances and depended on the particular organism and method used. SIANN detected each organism at high confidence, even at levels as low as 0.3% and 0.07% of the total.
Discussion
The process of detecting trace amounts of a specific organism in a complex mixture of DNA is challenging enough for an expert, but that pales in comparison to the difficulty of accomplishing the same certainty of detection in an automated manner. The results presented here show that SIANN rapidly detects the presence of a given set of organisms with a high degree of specificity and sensitivity. For example, at the 95% confidence (PPV) cutoff of 0.2, SIANN reliably detects all of the organisms tested here at as low as 0.3% abundance. This strong performance is likely due to the fact that SIANN is able to use a method (read alignment to whole genomes) that would be far too computationally costly if it were applied to the entire collection of known genomes. By focusing on a set of (customizable) target organisms and their near neighbors, SIANN can operate quickly and with low computational requirements while delivering highly accurate results.
SIANN is available on Illumina’s BaseSpace (www.basespace.illumina.com) as a NativeApp, with the database tested here (Appendix 1), as well as a database made from the NCBI representative set of prokaryotic genomes (ftp://ftp.ncbi.nlm.nih.gov/genomes/genome_reports/) (Appendix 2) and the complete set of NCBI viral genomes (ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/) (Appendix 3).
BaseSpace was chosen as an appropriate release platform because while the entire set of software and dependencies can be deployed by the user from within a graphical user interface, the actual computation takes place in a controlled ‘cloud’ environment. Such a distribution strategy obviates the need to satisfy the multiple software or OS dependencies that often arises with academic computational methods. Results for SIANN are compiled into a report format, showing both the organisms that surpass 95% confidence, as well as the closest strain match for each species. The default view masks the raw data output, so that the results are human-readable and do not present extraneous information. While the code for execution and database-construction on a users system is available from Signature Science, LLC, additional databases on the BaseSpace platform can be made available upon request.
There is a neverending list of questions that one could ask of metagenomic sequencing data generated from important samples. Instead of answering them all, we demonstrate a technique with a very narrow focus that is able to report with a high degree of confidence whether a given set of organisms is present in a sample. These results are presented to the user in a comprehensible format, and accessible on a commonly-used web platform. The world of bioinformatics will continue to progress and develop more sophisticated tools for metagenomic analysis, and we hope that the utility of SIANN will convince others to package and benchmark their tools in a way that they can be used with confidence by the larger public, as well as the research community.
Appendices
Appendix 1: Target Pathogen Database
Arenaviridae Arenavirus Golden-Gate-virus
Arenaviridae Arenavirus Lujo-virus
Arenaviridae Flexal-virus segment-L
Arenaviridae New-world-arenaviruses Allpahuayo-virus
Arenaviridae New-world-arenaviruses Chapare-virus
Arenaviridae New-world-arenaviruses Guanarito-virus
Arenaviridae New-world-arenaviruses Junin-virus
Arenaviridae New-world-arenaviruses Machupo-virus
Arenaviridae New-world-arenaviruses Sabia-virus
Arenaviridae New-world-arenaviruses Tacaribe-virus
Arenaviridae New-world-arenaviruses Whitewater-Arroyo-virus
Arenaviridae Old-world-arenaviruses Ippy-virus
Arenaviridae Old-world-arenaviruses Lassa-virus
Arenaviridae Old-world-arenaviruses Mopeia-virus-AN20410
Asfarviridae African-swine-fever-virus Benin-971-pathogenic-isolate
Asfarviridae African-Swine-Fever-Virus
Bacillus anthracis A2012 Bant 02 1
Bacillus anthracis Ames Ancestor
Bacillus anthracis Sterne
Bacillus cereus 03BB102
Bacillus cereus AH187
Bacillus cereus AH820
Bacillus cereus ATCC 14579
Bacillus cereus B4264
Bacillus cereus F65185
Bacillus cytotoxicus NVH 391-98
Bacillus mycoides DSM 2048
Bacillus mycoides Rock1-4
Bacillus thuringiensis BMB171
Bacillus thuringiensis Bt407
Bacillus thuringiensis HD-771
Bacillus thuringiensis serovar chinensis CT-43
Bacillus thuringiensis serovar konkukian 97-27
Brucella abortus A13334
Brucella ceti B1 94
Brucella ceti M13 05 1 supercont1 22
Brucella melitensis ATCC 23457
Brucella melitensis bv 1 str 16M
Brucella ovis ATCC 25840
Brucella suis 1330
Brucella suis ATCC 23445
Bunyaviridae Akabane-virus segment-M
Bunyaviridae Hantavirus Andes-virus
Bunyaviridae Hantavirus Dobrava-Belgrade-virus-strain-DOBV-Ano-Poroia-Afl9-1999
Bunyaviridae Hantavirus Hantaan-virus
Bunyaviridae Hantavirus Puumala-virus
Bunyaviridae Hantavirus Seoul-virus-strain-Seoul-80-39-clone-1
Bunyaviridae Hantavirus Sin-Nombre-virus
Bunyaviridae Hantavirus Thottapalayam-virus
Bunyaviridae Hantavirus Tula-virus
Bunyaviridae Nairovirus Crimean-Congo-hemorrhagic-fever-virus
Bunyaviridae Nairovirus Dugbe-virus
Bunyaviridae Phlebovirus Rift-Valley-fever-virus
Burkholderia cenocepacia HI2424
Burkholderia cenocepacia J2315
Burkholderia cenocepacia MC0-3
Burkholderia cepacia GG4
Burkholderia gladioli BSR3
Burkholderia glumae BGR1
Burkholderia mallei 2002721280
Burkholderia mallei ATCC 10399
Burkholderia mallei NCTC 10247
Burkholderia mallei SAVP1
Burkholderia multivorans ATCC 17616
Burkholderia oklahomensis C6786
Burkholderia oklahomensis EO147
Burkholderia pseudomallei 1026b
Burkholderia pseudomallei 1106a
Burkholderia pseudomallei 1710b
Burkholderia pseudomallei 668
Burkholderia pseudomallei BPC006
Burkholderia pseudomallei K96243
Burkholderia pyrrocinia CH-67
Burkholderia thailandensis ATCC 700388
Burkholderia thailandensis E264
Burkholderia thailandensis MSMB121
Campylobacter coli JV20 Campylobacter fetus subsp fetus 82-40
Campylobacter jejuni RM1221
Campylobacter jejuni subsp doylei 26997
Campylobacter jejuni subsp jejuni 81-176
Campylobacter jejuni subsp jejuni NCTC 11168 ATCC 700819
Campylobacter upsaliensis JV21
Clostridium acetobutylicum DSM 1731
Clostridium botulinum A str ATCC 3502
Clostridium botulinum BKT015925
Clostridium botulinum B str Eklund 17B
Clostridium botulinum E3 str Alaska E43
Clostridium botulinum F str 230613
Clostridium botulinum H04402 065
Clostridium difficile 2007855
Clostridium difficile 630
Clostridium difficile BI1
Clostridium difficile BI9
Clostridium perfringens ATCC 13124
Clostridium perfringens SM101
Clostridium perfringens str 13
Clostridium symbiosum WAL-14163
Clostridium symbiosum WAL-14673
Clostridium tetani E88
Clostridium thermocellum ATCC 27405
Clostridium thermocellum DSM 1313
Clostridium tunisiense TJ C661
Clostridium ultunense Esp
Coccidioides immitis H5384
Coccidioides immitis RMSCC 2394
Coccidioides immitis RS
Coccidioides posadasii C735 delta SOWgp
Coccidioides posadasii CPA 0001
Coccidioides posadasii CPA 0020
Coronaviridae Alphacoronavirus Bat-coronavirus-HKU2
Coronaviridae Alphacoronavirus Feline-infectious-peritonitis-virus
Coronaviridae Alphacoronavirus Human-coronavirus-229E
Coronaviridae Alphacoronavirus TGEV-Purdue-P115
Coronaviridae Bafinivirus White-bream-virus
Coronaviridae Betacoronavirus Bovine-coronavirus
Coronaviridae Betacoronavirus Murine-hepatitis-virus-strain-A59
Coronaviridae Betacoronavirus Murine-hepatitis-virus-strain-JHM
Coronaviridae Betacoronavirus SARS-coronavirus
Coronaviridae Coronavirinae Munia-coronavirus-HKU13-3514
Coronaviridae Gammacoronavirus Avian-infectious-bronchitis-virus
Coronaviridae Gammacoronavirus Turkey-coronavirus
Coronaviridae Torovirus Breda-virus
Coronaviridae unclassified-coronaviruses Bat-coronavirus-BM48-31-BGR-2008
Coronaviridae unclassified-coronaviruses Bovine-respiratory-coronavirus-AH187
Coronaviridae unclassified-coronaviruses Human-enteric-coronavirus-strain-4408
Coxiella burnetii CbuG Q212
Coxiella burnetii Dugway 5J108 111
Coxiella burnetii RSA 493 Diplorickettsia massiliensis 20B CS 1
Ehrlichia canis str Jake Ehrlichia chaffeensis str Arkansas
Ehrlichia chaffeensis str Sapulpa ctg90
Ehrlichia ruminantium str Gardel
Ehrlichia ruminantium str Welgevonden
Escherichia coli APEC O1
Escherichia coli BL21 DE3
Escherichia coli B str REL606
Escherichia coli ETEC H10407
Escherichia coli O104H4 str 2011C-3493
Escherichia coli O157H7 str EC4115
Escherichia coli O157H7 str Sakai
Escherichia coli O7K1 str CE10
Escherichia coli O83H1 str NRG 857C
Escherichia coli str K-12 substr MG1655
Filoviridae Ebolavirus Bundibugyo-ebolavirus
Filoviridae Ebolavirus Cote-dIvoire-ebolavirus
Filoviridae Ebolavirus Ebola-virus-Mayinga-Zaire
Filoviridae Ebolavirus Reston-ebolavirus
Filoviridae Ebolavirus Sudan-ebolavirus
Filoviridae Marburgvirus Lake-Victoria-marburgvirus-Musoke
Flaviviridae Alkhurma-virus
Flaviviridae Classical-swine-fever-virus
Flaviviridae Dengue-virus 1
Flaviviridae Dengue-virus 2
Flaviviridae Dengue-virus 3
Flaviviridae Dengue-virus 4
Flaviviridae Japanese-encephalitis-virus genome
Flaviviridae Karshi-virus
Flaviviridae Langat-virus
Flaviviridae Louping-ill-virus
Flaviviridae Murray-Valley-encephalitis-virus
Flaviviridae Omsk-hemorrhagic-fever-virus
Flaviviridae Powassan-virus
Flaviviridae St-Louis-encephalitis-virus
Flaviviridae Tick-borne-encephalitis-virus
Flaviviridae Usutu-virus
Flaviviridae West-Nile-virus
Flaviviridae Yellow-fever-virus
Francisella cf novicida Fx1
Francisella noatunensis subsp orientalis str Toba 04
Francisella novicida U112
Francisella philomiragia subsp philomiragia ATCC 25015
Francisella philomiragia subsp philomiragia ATCC 25017
Francisella tularensis subsp holarctica F92
Francisella tularensis subsp mediasiatica FSC147
Francisella tularensis subsp tularensis FSC198
Herpesviridae Alcelaphine-herpesvirus 1
Herpesviridae Macacine-herpesvirus 1
Listeria fleischmannii LU2006-1 c88
Listeria innocua Clip11262
Listeria innocua FSL J1-023
Listeria ivanovii FSL F6-596
Listeria ivanovii subsp ivanovii PAM 55
Listeria marthii FSL S4-120
Listeria monocytogenes 07PF0776
Listeria monocytogenes 08-5578
Listeria monocytogenes 10403S
Listeria monocytogenes ATCC 19117
Listeria monocytogenes Finland 1998
Listeria monocytogenes FSL R2-561
Listeria monocytogenes La111
Listeria seeligeri FSL N1-067
Listeria seeligeri serovar 12b str SLCC3954
Listeria welshimeri serovar 6b str SLCC5334
Paramyxoviridae Avulavirus Newcastle-disease-virus-B1
Paramyxoviridae Henipavirus Hendra-virus
Paramyxoviridae Henipavirus Nipah-virus
Paramyxoviridae Menangle-virus
Paramyxoviridae Morbillivirus Measles-virus
Paramyxoviridae Peste-des-petits-ruminants-virus
Paramyxoviridae Respirovirus Human-parainfluenza-virus-1
Paramyxoviridae Respirovirus Human-parainfluenza-virus-3
Paramyxoviridae Respirovirus Sendai-virus
Paramyxoviridae Rinderpest-virus strain-Kabete-O
Paramyxoviridae Rubulavirus Human-parainfluenza-virus-2
Paramyxoviridae Rubulavirus Human-parainfluenza-virus-4a
Paramyxoviridae Rubulavirus Mumps-virus
Picornaviridae Foot-and-mouth-disease-virus -type-O
Picornaviridae Swine-vesicular-disease-virus strain-HK70
Picornaviridae Swine-vesicular-disease-virus strain-NET192
Poxviridae Avipoxvirus Fowlpox-virus
Poxviridae Crocodylidpoxvirus Nile-crocodilepox-virus
Poxviridae Goatpox-virus Pellor
Poxviridae Leporipoxvirus Myxoma-virus
Poxviridae Lumpy-skin-disease-virus NI-2490
Poxviridae Molluscipoxvirus Molluscum-contagiosum-virus-subtype-1
Poxviridae Orthopoxvirus Camelpox-virus
Poxviridae Orthopoxvirus Cowpox-virus
Poxviridae Orthopoxvirus Ectromelia-virus
Poxviridae Orthopoxvirus Monkeypox-virus-Zaire-96-I-16
Poxviridae Orthopoxvirus Taterapox-virus
Poxviridae Orthopoxvirus Vaccinia-virus
Poxviridae Orthopoxvirus Variola-virus
Poxviridae Sheeppox-virus 17077-99
Poxviridae Suipoxvirus Swinepox-virus
Puccinia graminis f sp tritici CRL 75-36-700-3
Ralstonia pickettii 12D
Ralstonia pickettii 12J
Ralstonia solanacearum CFBP2957
Ralstonia solanacearum CMR15
Ralstonia solanacearum GMI1000
Rathayibacter toxicus DSM 7488
Reoviridae African-horsesickness-virus segment-10
Rhabdoviridae Vesicular-stomatitis-Indiana-virus
Rhabdoviridae Vesicular-stomatitis-virus strain-NJ2075212NM
Rickettsia bellii OSU 85-389
Rickettsia conorii str Malish 7
Rickettsia prowazekii str Breinl
Rickettsia prowazekii str RpGvF24
Rickettsia rickettsii str Arizona
Rickettsia typhi str B9991CWPP
Rickettsiella grylli gcontig 634
Salmonella bongori N268-08
Salmonella bongori NCTC 12419
Salmonella enterica subsp arizonae serovar 62z4z23-str RSK2980
Salmonella enterica subsp enterica serovar Dublin str CT 02021853
Salmonella enterica subsp enterica serovar Newport str SL254
Salmonella enterica subsp enterica serovar Paratyphi A str ATCC 9150
Salmonella enterica subsp enterica serovar Typhimurium str LT2
Salmonella enterica subsp enterica serovar Typhi str Ty2
Shigella boydii CDC 3083-94
Shigella boydii Sb227
Shigella dysenteriae Sd197
Shigella flexneri 2002017
Shigella flexneri 2a str 2457T
Shigella flexneri 2a str 301
Shigella flexneri 5 str 8401
Shigella sonnei 53G
Shigella sonnei Ss046
Staphylococcus arlettae CVD059 SARL c230
Staphylococcus aureus 04-02981
Staphylococcus aureus 08BA02176
Staphylococcus aureus subsp aureus N315
Staphylococcus aureus subsp aureus NCTC 8325
Staphylococcus aureus subsp aureus TW20
Staphylococcus capitis QN1 Contig63
Staphylococcus capitis SK14
Staphylococcus caprae C87
Staphylococcus carnosus subsp carnosus TM300
Staphylococcus epidermidis ATCC 12228
Staphylococcus epidermidis RP62A
Staphylococcus equorum subsp equorum Mu2
Staphylococcus haemolyticus JCSC1435
Staphylococcus hominis SK119
Staphylococcus hominis subsp hominis C80
Staphylococcus lugdunensis HKU09-01
Staphylococcus lugdunensis N920143
Togaviridae Alphavirus Barmah-Forest-virus Togaviridae Chikungunya-virus
Togaviridae EEEV-complex Eastern-equine-encephalitis-virus
Togaviridae Rubivirus Rubella-virus
Togaviridae SFV-complex O-nyong-nyong-virus
Togaviridae Venezuelan-equine-encephalitis-virus
Togaviridae WEEV-complex Sindbis-virus
Togaviridae Western-equine-encephalomyelitis-virus
Xanthomonas albilineans GPE PC73
Xanthomonas axonopodis Xac29-1
Xanthomonas oryzae pv oryzae KACC 10331
Xanthomonas oryzae pv oryzae MAFF 311018
Xanthomonas oryzae pv oryzae PXO99A
Xanthomonas vasicola pv vasculorum NCPPB 1326 scf 9767 4580
Yersinia aldovae ATCC 35236
Yersinia bercovieri ATCC 43970
Yersinia enterocolitica IP 10393
Yersinia enterocolitica IP2222
Yersinia enterocolitica subsp enterocolitica 8081
Yersinia enterocolitica subsp palearctica 105 5R
Yersinia frederiksenii ATCC 33641
Yersinia intermedia ATCC 29909
Yersinia kristensenii ATCC 33638
Yersinia mollaretii ATCC 43969
Yersinia pestis A1122
Yersinia pestis Antiqua
Yersinia pestis KIM 10
Yersinia pestis Pestoides F
Yersinia pseudotuberculosis IP 31758
Yersinia pseudotuberculosis IP 32953
Yersinia pseudotuberculosis PB1
Yersinia pseudotuberculosis YPIII
Yersinia rohdei ATCC 43380
Yersinia ruckeri ATCC 29473
Appendix 2: Viral Database
Abaca bunchy top virus DNA-C
Abaca bunchy top virus DNA-M
Abaca bunchy top virus DNA-N
Abaca bunchy top virus DNA-R
Abaca bunchy top virus DNA-S
Abaca bunchy top virus segment 2
Abalone shriveling syndrome-associated virus
Abutilon Brazil virus DNA A
Abutilon Brazil virus DNA B
Abutilon mosaic virus DNA A
Abutilon mosaic virus DNA B
Acanthocystis turfacea Chlorella virus 1
Acheta domesticus densovirus
Acholeplasma phage L2
Acholeplasma phage MV-L1
Acidianus bottle-shaped virus
Acidianus filamentous virus 1
Acidianus filamentous virus 2
Acidianus filamentous virus 3
Acidianus filamentous virus 6
Acidianus filamentous virus 7
Acidianus filamentous virus 8
Acidianus filamentous virus 9
Acidianus rod-shaped virus 1
Acidianus spindle-shaped virus 1
Acidianus two-tailed virus
Actinomyces phage Av-1
Actinoplanes phage phiAsp2
Acyrthosiphon pisum bacteriophage APSE-1
Adeno-associated virus-1
Adeno-associated virus-2
Adeno-associated virus-3
Adeno-associated virus-4
Adeno-associated virus 5
Adeno-associated virus-7
Adeno-associated virus-8
Adoxophyes honmai NPV
Adoxophyes orana granulovirus
Adoxophyes orana nucleopolyhedrovirus
Aedes aegypti densovirus
Aedes albopictus densovirus
Aedes taeniorhynchus iridescent virus
Aeromonas phage 25
Aeromonas phage 31
Aeromonas phage 44RR2.8t
Aeromonas phage Aeh1
Aeromonas phage phiO18P african cassava mosaic virus DNA A african cassava mosaic virus DNA B
African green monkey polyomavirus
African swine fever virus
Ageratum enation virus
Ageratum leaf Cameroon betasatellite
Ageratum leaf curl virus-G52
Ageratum yellow vein China virus-associated DNA beta
Ageratum yellow vein Chinavirus
Ageratum yellow vein Hualian virus-TaiwanHsinchutom2003 DNA A
Ageratum yellow vein Sri Lanka virus segment A
Ageratum yellow vein Taiwan virus
Ageratum yellow vein virusassociated DNA beta
Ageratum yellow veinvirus
Agrotis ipsilon multiple nucleopolyhedrovirus
Agrotis segetum granulovirus
Agrotis segetum nucleopolyhedrovirus
Alcelaphine herpesvirus 1
Aleutian mink disease virus
Allamanda leaf curl virus DNA-A
Alternanthera yellow vein virus DNA-A
Alternanthera yellow vein virus satellite DNA beta
Ambystoma tigrinum virus
Amsacta moorei entomopoxvirus L
Anguillid herpesvirus 1
Anopheles gambiae densonucleosis virus
Antheraea pernyi nucleopolyhedrovirus
Anticarsia gemmatalis nucleopolyhedrovirus
Archaeal BJ1 virus
Ateline herpesvirus 3
Autographa californica nucleopolyhedrovirus
Avian adeno-associated virus
ATCC VR-865
Avian adeno-associated virus strain DA-1
Avian endogenous retrovirus EAV-HP
Azospirillum phage Cd
Bacillus phage 0305phi8-36
Bacillus phage AP50
Bacillus phage B103
Bacillus phage Bam35c
Bacillus phage BCJA1c
Bacillus phage Cherry
Bacillus phage Fah
Bacillus phage GA-1
Bacillus phage Gamma
Bacillus phage GIL16c
Bacillus phage IEBH
Bacillus phage phi105
Bacillus phage phi29
Bacillus phage SPBc2
Bacillus phage SPO1
Bacillus phage SPP1
Bacillus phage TP21-L
Bacillus phage WBeta
Bacillus prophage phBC6A51
Bacillus prophage phBC6A52
Bacillus virus 1
Bacteriophage Aaphi23
Bacteriophage APSE-2
Bacteriophage PSA
Bacteriophage RB32
Bacteroides phage B40-8
Banana bunchy top virus DNA C
Banana bunchy top virus DNA M
Banana bunchy top virus DNA N
Banana bunchy top virus DNA R
Banana bunchy top virus DNA S
Banana bunchy top virus DNA U3
Banana streak GF virus
Banana streak Mysore virus
Banana streak OL virus
Banana streak virus genome
Banana streak virus strain Acuminata Vietnam
Bandicoot papillomatosis carcinomatosis virus type 1
Bandicoot papillomatosis carcinomatosis virus type 2
Bat adeno-associated virus YNM
Bdellovibrio phage phiMH2K
Beak and feather disease virus
Bean calico mosaic virus DNA A
Bean calico mosaic virus DNA B
Bean dwarf mosaic virus DNA A
Bean dwarf mosaic virus DNA B
Bean golden mosaic virus DNA A
Bean golden mosaic virus DNA B
Bean golden yellow mosaic virus DNA A
Bean golden yellow mosaic virus DNA B
Bean yellow dwarf virus putative genes V1
Beet curly top Iran virus-K
Beet curly top virus-California Logan
Beet mild curly top virus-Worland4
Beet severe curly top virus-Cfh
Begomovirus-associated DNA II
Begomovirus-associated DNA-III
Bettongia penicillata papillomavirus 1
Bhendi yellow vein
Bhubhaneswar virus DNA-A
Bhendi yellow vein Delhi virus 2004New Delhi DNA-A
Bhendi yellow vein mosaic virus-associated DNA beta
Bhendi yellow vein mosaic Virus
Bitter gourd leaf curl disease-associated DNA beta
BK polyomavirus
Blainvillea yellow spot virus DNA-A
Blainvillea yellow spot virus DNA-B
Blattella germanica densovirus
Blueberry red ringspot virus
Bocavirus gorillaGBoV12009
Bombyx mandarina nucleopolyhedrovirus
Bombyx mori densovirus 5
Bombyx mori NPV
Bordetella phage BIP-1
Bordetella phage BMP-1
Bordetella phage BPP-1
Bougainvillea spectabilis chlorotic vein-banding virus
Bovine adeno-associated virus
Bovine adenovirus A
Bovine adenovirus B
Bovine adenovirus D
Bovine ephemeral fever virus
Bovine foamy virus
Bovine herpesvirus 1
Bovine herpesvirus 4 long unique region
Bovine herpesvirus 5
Bovine papillomavirus-1
Bovine papillomavirus 3
Bovine papular stomatitis virus
Bovine parvovirus 2
Bovine Parvovirus
Bovine polyomavirus
Burkholderia ambifaria phage BcepF1
Burkholderia phage Bcep 176
Burkholderia phage Bcep1
Burkholderia phage Bcep22
Burkholderia phage Bcep43
Burkholderia phage Bcep781
Burkholderia phage BcepB1A
Burkholderia phage BcepC6B
Burkholderia phage BcepGomr
Burkholderia phage BcepIL02
Burkholderia phage BcepMu
Burkholderia phage BcepNazgul
Burkholderia phage BcepNY3
Burkholderia phage KS10
Burkholderia phage KS9
Burkholderia phage phi1026b
Burkholderia phage phi644-2 chromosome
Burkholderia phage phiE12-2 chromosome
Burkholderia phage phiE125
Burkholderia phage phiE202 chromosome
Burkholderia phage phiE255 chromosome
Burkholderia prophage phi52237
Cabbage leaf curl virus DNA A
Cabbage leaf curl virus DNA B
Cacao swollen shoot virus
California sea lion anellovirus
California sea lion polyomavirus 1
Callitrichine herpesvirus 3 strain CJ0149
Camelpox virus
Campoletis sonorensis ichnovirus chromosome segment W
Campoletis sonorensis ichnovirus segment B
Campoletis sonorensis ichnovirus segment C
Campoletis sonorensis ichnovirus segment D
Campoletis sonorensis ichnovirus segment E
Campoletis sonorensis ichnovirus segment F
Campoletis sonorensis ichnovirus segmentG2
Campoletis sonorensis ichnovirus segment G
Campoletis sonorensis ichnovirus segment H
Campoletis sonorensis ichnovirus segmentI2
Campoletis sonorensis ichnovirus segment I
Campoletis sonorensis ichnovirus segment J
Campoletis sonorensis ichnovirus segment L
Campoletis sonorensis ichnovirus segment M
Campoletis sonorensis ichnovirus segment N
Campoletis sonorensis ichnovirus segment O1
Campoletis sonorensis ichnovirus segment P
Campoletis sonorensis ichnovirus segment Q
Campoletis sonorensis ichnovirus segment T
Campoletis sonorensis ichnovirus segment U
Campoletis sonorensis ichnovirus segment V
Campoletis sonorensis ichnovirus segment Z
Campoletis sonorensis ichnovirus superhelical segment A
Campoletis sonorensis ichnovirus superhelical segment aprime
Canary circovirus
Canarypox virus
Canine adenovirus Canine minute virus
Canine oral papillomavirus
Canine papillomavirus 2
Canine papillomavirus 3
Canine papillomavirus 4
Canine papillomavirus 6
Canine parvovirus
Capra hircus papillomavirus type 1
Cardiospermum yellow leaf curl virus satellite DNA beta
Caretta caretta papillomavirus 1
Carnation etched ring virus
Casphalia extranea densovirus
Cassava vein mosaic virus
Cauliflower mosaic virus
Cercopithecine herpesvirus 2
Cercopithecine herpesvirus 5 strain 2715
Cercopithecine herpesvirus 9
Cestrum yellow leaf curling virus
Chaetoceros salsugineum DNA virus
Chayote yellow mosaic virus
Chicken anemia virus
Chickpea chlorotic dwarf virus
Chilli leaf curl disease associated sequence virion
Chilli leaf curl Multan alphasatellite
Chilli leaf curl virus
Chino del tomate virus DNA A
Chino del tomate virus DNA B
Chlamydia phage 3
Chlamydia phage 4
Chlamydia phage Chp1
Chlamydia phage Chp2
Chlamydia phage PhiCPG1
Chloris striate mosaic virus
Choristoneura fumiferana DEF MNPV
Choristoneura fumiferana MNPV
Choristoneura occidentalis granulovirus
Chrysodeixis chalcites nucleopolyhedrovirus
Circovirus-like genome BBC-A
Circovirus-like genome CB-A
Circovirus-like genome CB-B
Circovirus-like genome RW-A
Circovirus-like genome RW-B
Circovirus-like genome RW-C
Circovirus-like genome RW-D
Circovirus-like genome RW-E
Circovirus-like genome SAR-A
Circovirus-like genome SAR-B
Citrus psorosis virus RNA1
Citrus psorosis virus RNA2
Citrus psorosis virus RNA3
Citrus yellow mosaic virus
Clanis bilineata nucleopolyhedrosis virus
Clavibacter phage CMP1
Clerodendron yellow mosaic virus
Clerodendrum golden mosaic
China virus DNA A
Clerodendrum golden mosaic
China virus DNA B
Clerodendrum golden mosaic virus DNA-A
Clerodendrum golden mosaic virus DNA-B
Clostridium phage 39-O
Clostridium phage c-st
Clostridium phage phi3626
Clostridium phage phiC2
Clostridium phage phi CD119
Clostridium phage phiCD27
Clostridium phage phiCTP1
Coconut foliar decay virus
Columbid circovirus
Commelina yellow mottle virus
Corchorus golden mosaic virus DNA-A
Corchorus golden mosaic virus DNA-B
Corchorus yellow spot virus DNA A
Corchorus yellow spot virus DNA B
Corchorus yellow vein virus-Hoa Binh DNA A
Corchorus yellow vein virus-Hoa Binh DNA B
Corynebacterium phage BFK20
Corynebacterium phage P1201
Cotesia congregata bracovirus segment Circle10
Cotesia congregata bracovirus segment Circle11
Cotesia congregata bracovirus segment Circle12
Cotesia congregata bracovirus segment Circle13
Cotesia congregata bracovirus segment Circle14
Cotesia congregata bracovirus segment Circle15
Cotesia congregata bracovirus segment Circle17
Cotesia congregata bracovirus segment Circle19
Cotesia congregata bracovirus segment circle1
Cotesia congregata bracovirus segment Circle20
Cotesia congregata bracovirus segment Circle21
Cotesia congregata bracovirus segment Circle22
Cotesia congregata bracovirus segment Circle23
Cotesia congregata bracovirus segment Circle25
Cotesia congregata bracovirus segment Circle26
Cotesia congregata bracovirus segment circle2
Cotesia congregata bracovirus segment Circle30
Cotesia congregata bracovirus segment Circle31
Cotesia congregata bracovirus segment Circle32
Cotesia congregata bracovirus segment Circle33
Cotesia congregata bracovirus segment Circle35
Cotesia congregata bracovirus segment Circle36
Cotesia congregata bracovirus segment circle3
Cotesia congregata bracovirus segment Circle4
Cotesia congregata bracovirus segment Circle5
Cotesia congregata bracovirus segment Circle9
Cotesia congregata virus segment Circle18
Cotesia congregata virus segment Circle6
Cotesia congregata virus segment Circle7
Cotesia congregata virus segment Circle8
Cotton leaf crumple geminivirus DNA B
Cotton leaf crumple virus DNA A
Cotton leaf curl Alabad virus
Cotton leaf curl Bangalore virus-associated DNA beta
Cotton leaf curl Bangalore virus segment A
Cotton leaf curl Burewala alphasatellite
Cotton leaf curl Burewala betasatellite
Cotton leaf curl Burewala virus-IndiaVehari2004
Cotton leaf curl Gezira alphasatellite
Cotton leaf curl Gezira beta
Cotton leaf curl Gezira Betasatellite extrachromosomal
Cotton leaf curl Gezira virus
Cotton leaf curl Kokhran virus
Cotton leaf curl Multan Virus
Cotton leaf curl Multan virus satellite DNA beta
Cotton leaf curl Multan virus satellite U36-1
Cotton leaf curl Rajasthan virus segment A
Cotton leaf curl virus-associated DNA beta
Cottontail rabbit papillomavirus
Cowpea severe leaf curl-associated DNA beta
Cowpox virus Crassocephalum yellow vein virus-Jinghong
Croton yellow vein mosaic alphasatellite
Croton yellow vein mosaic virus
Croton yellow vein mosaic Virus satellite DNA beta
Croton yellow vein virus Crow polyomavirus
Cryptophlebia leucotreta granulovirus
Cucurbita yellow vein virus-associated DNA beta
Cucurbit leaf crumple virus DNA A
Cucurbit leaf crumple virus DNA B
Culex nigripalpus NPV
Culex pipiens densovirus Cyanophage PSS2
Cyanophage Syn5 Cycad leaf necrosis virus
Cydia pomonella granulovirus
Cyprinid herpesvirus 3
Deer papillomavirus
Deerpox virus W-1170-84
Deerpox virus W-848-83
Deftia phage phiW-14
Dendrolimus punctatus densovirus
Desmodium leaf distortion virus DNA A
Desmodium leaf distortion virus DNA B
Diadromus pulchellus ascovirus 4a
Diatraea saccharalis densovirus
Dicliptera yellow mottle virus DNA A
Dicliptera yellow mottle virus DNA B
Digitaria streak virus
Dioscorea bacilliform virus
Dolichos yellow mosaic virus
Dracaena mottle virus
Duck adenovirus A
Duck circovirus
Duck hepatitis B virus
East African cassava mosaic Cameroon virus DNA A
East African cassava mosaic Cameroon virus DNA B
East African cassava mosaic Kenya virus DNA A
East African cassava mosaic Kenya virus DNA B
East African cassava mosaic virus DNA A
East African cassava mosaic virus DNA B
East African cassava mosaic Zanzibar virus DNA-A
East African cassava mosaic Zanzibar virus DNA B
Ecotropis obliqua NPV
Ectocarpus siliculosus virus 1
Ectromelia virus
Emiliania huxleyi virus 86
Emilia yellow vein virus-associated DNA beta
Emilia yellow vein virus-Fz1
Enterobacteria phage 13a
Enterobacteria phage 933W
Enterobacteria phage alpha3
Enterobacteria phage BA14
Enterobacteria phage BP-4795
Enterobacteria phage EcoDS1
Enterobacteria phage EPS7
Enterobacteria phage epsilon15
Enterobacteria phage ES18
Enterobacteria phage Felix 01
Enterobacteria phage Fels-2
Enterobacteria phage G4
Enterobacteria phage HK022
Enterobacteria phage HK620
Enterobacteria phage HK97
Enterobacteria phage I2-2
Enterobacteria phage ID18
Enterobacteria phage ID2 MoscowID2001
Enterobacteria phage If1
Enterobacteria phage Ike
Enterobacteria phage IME08
Enterobacteria phage JK06
Enterobacteria phage JS10
Enterobacteria phage JS98
Enterobacteria phage JSE
Enterobacteria phage K1-5
Enterobacteria phage K1E
Enterobacteria phage K1F
Enterobacteria phage lambda
Enterobacteria phage LKA1
Enterobacteria phage M13
Enterobacteria phage Min27
Enterobacteria phage Mu
Enterobacteria phage N15
Enterobacteria phage N4
Enterobacteria phage P1
Enterobacteria phage P22 virus
Enterobacteria phage P2 virus
Enterobacteria phage P4
Enterobacteria phage Phi1
Enterobacteria phage phiEco32
Enterobacteria phage phiEcoM-GJ1
Enterobacteria phage phiP27
Enterobacteria phage phiX174 sensu lato
Enterobacteria phage PRD1
Enterobacteria phage PsP3
Enterobacteria phage RB14
Enterobacteria phage RB16
Enterobacteria phage RB43
Enterobacteria phage RB49
Enterobacteria phage RB51
Enterobacteria phage RB69
Enterobacteria phage RTP
Enterobacteria phage Sf6
Enterobacteria phage SfV
Enterobacteria phage SP6
Enterobacteria phage SSL-2009a
Enterobacteria phage ST104
Enterobacteria phage St-1
Enterobacteria phage ST64T
Enterobacteria phage T1
Enterobacteria phage T3
Enterobacteria phage T4
Enterobacteria phage T5
Enterobacteria phage T7
Enterobacteria phage TLS
Enterobacteria phage VT2-Sakai
Enterobacteria phage WA13
Enterobacteria phage WV8
Enterobacteria phage YYZ-2008
Enterococcus faecalis 62 chromosome
Enterococcus faecalis 62 plasmid EF62pA
Enterococcus faecalis 62 plasmid EF62pB
Enterococcus faecalis 62 plasmid EF62pC
Enterococcus phage EF62phi
Enterococcus phage EFAP-1
Enterococcus phage phiEf11
Enterococcus phage phiEF24C
Enterococcus phage phiFL1A
Enterococcus phage phiFL2A
Enterococcus phage phiFL3A
Enterococcus phage phiFL4A
Enzootic nasal tumour virus of goats
Epiphyas postvittana NPV
Equid herpesvirus 1
Equid herpesvirus 2
Equid herpesvirus 4
Equid herpesvirus 9
Equine papillomavirus 2
Eragrostis curvula streak virus
Eragrostis streak virus
Erectites yellow mosaic virus DNA-A
Erectites yellow mosaic virus satellite DNA beta
Erethizon dorsatum papillomavirus type 1
Erinaceus europaeus papillomavirus
Erwinia amylovora phage Era103
Erwinia phage phiEa21-4
Escherichia coli bacteriophage rv5
Escherichia phage D108
Escherichia phage phiV10
Eupatorium vein clearing virus
Eupatorium yellow vein associated DNA beta
Eupatorium yellow vein virus
Euphorbia leaf curl virus DNA A
Euphorbia yellow mosaic virus DNA A
Euphorbia yellow mosaic virus DNA B
Euproctis pseudoconspersa nucleopolyhedrovirus
European elk papillomavirus
Faba bean necrotic stunt virus DNA C
Faba bean necrotic stunt virus DNA M
Faba bean necrotic stunt virus DNA N
Faba bean necrotic stunt virus DNA R
Faba bean necrotic stunt virus DNA S
Faba bean necrotic stunt virus DNA U1
Faba bean necrotic stunt virus DNA U2
Faba bean necrotic stunt virus DNA U4
Faba bean necrotic yellows virus DNA 10
Faba bean necrotic yellows virus DNA-1
Faba bean necrotic yellows virus DNA 2
Faba bean necrotic yellows virus DNA 4
Faba bean necrotic yellows virus DNA 5
Faba bean necrotic yellows virus DNA 7
Faba bean necrotic yellows virus DNA 8
Faba bean necrotic yellows virus DNA 9
Faba bean necrotic yellows Virus
Feldmannia species virus Felid herpesvirus 1
Felis domesticus papillomavirus type 1
Fenneropenaeus chinensis hepatopancreatic densovirus
Figwort mosaic virus
Finch circovirus Finch polyomavirus
Flavobacterium phage 11b
Fowl adenovirus A
Fowl adenovirus D
Fowlpox virus
Francolinus leucoscepus papillomavirus 1
Fringilla coelebs papillomavirus
Frog adenovirus 1
Frog virus 3
Galleria mellonella densovirus
Gallid herpesvirus 1
Gallid herpesvirus 2
Gallid herpesvirus 3
Gammapapillomavirus HPV127
Geobacillus phage
GBSV1 Geobacillus virus E2
Glossina pallidipes salivary gland hypertrophy virus
Glypta fumiferanae ichnovirus segmentA10
Glypta fumiferanae ichnovirus segment A1
Glypta fumiferanae ichnovirus segment A2
Glypta fumiferanae ichnovirus segment A3
Glypta fumiferanae ichnovirus segment A4
Glypta fumiferanae ichnovirus segment A5
Glypta fumiferanae ichnovirus segment A6
Glypta fumiferanae ichnovirus segment A7
Glypta fumiferanae ichnovirus segment A8
Glypta fumiferanae ichnovirus segment A9
Glypta fumiferanae ichnovirus segment B10
Glypta fumiferanae ichnovirus segment B11
Glypta fumiferanae ichnovirus segment B12
Glypta fumiferanae ichnovirus segment B13
Glypta fumiferanae ichnovirus segment B14
Glypta fumiferanae ichnovirus segment B15
Glypta fumiferanae ichnovirus segment B16
Glypta fumiferanae ichnovirus segment B17
Glypta fumiferanae ichnovirus segment B18
Glypta fumiferanae ichnovirus segment B19
Glypta fumiferanae ichnovirus segment-B1
Glypta fumiferanae ichnovirus segment B20
Glypta fumiferanae ichnovirus segment B21
Glypta fumiferanae ichnovirus segment B22
Glypta fumiferanae ichnovirus segment B23
Glypta fumiferanae ichnovirus segment B24
Glypta fumiferanae ichnovirus segment B25
Glypta fumiferanae ichnovirus segment B26
Glypta fumiferanae ichnovirus segment B27
Glypta fumiferanae ichnovirus segment B28
Glypta fumiferanae ichnovirus segment B29
Glypta fumiferanae ichnovirus segment-B2
Glypta fumiferanae ichnovirus segment B30
Glypta fumiferanae ichnovirus segment B31
Glypta fumiferanae ichnovirus segment B32
Glypta fumiferanae ichnovirus segment B33
Glypta fumiferanae ichnovirus segment B34
Glypta fumiferanae ichnovirus segment B35
Glypta fumiferanae ichnovirus segment B36
Glypta fumiferanae ichnovirus segment B37
Glypta fumiferanae ichnovirus segment B38
Glypta fumiferanae ichnovirus segment B39
Glypta fumiferanae ichnovirus segment-B3
Glypta fumiferanae ichnovirus segment B40
Glypta fumiferanae ichnovirus segment B41
Glypta fumiferanae ichnovirus segment B42
Glypta fumiferanae ichnovirus segment B43
Glypta fumiferanae ichnovirus segment B44
Glypta fumiferanae ichnovirus segment B45
Glypta fumiferanae ichnovirus segment B46
Glypta fumiferanae ichnovirus segment B47
Glypta fumiferanae ichnovirus segment B48
Glypta fumiferanae ichnovirus segment B49
Glypta fumiferanae ichnovirus segment-B4
Glypta fumiferanae ichnovirus segment B50
Glypta fumiferanae ichnovirus segment B51
Glypta fumiferanae ichnovirus segment B52
Glypta fumiferanae ichnovirus segment B53
Glypta fumiferanae ichnovirus segment B54
Glypta fumiferanae ichnovirus segment B55
Glypta fumiferanae ichnovirus segment B56
Glypta fumiferanae ichnovirus segment B57
Glypta fumiferanae ichnovirus segment B58
Glypta fumiferanae ichnovirus segment B59
Glypta fumiferanae ichnovirus segment-B5
Glypta fumiferanae ichnovirus segment B60
Glypta fumiferanae ichnovirus segment B61
Glypta fumiferanae ichnovirus segment B62
Glypta fumiferanae ichnovirus segment B63
Glypta fumiferanae ichnovirus segment B64
Glypta fumiferanae ichnovirus segment B65
Glypta fumiferanae ichnovirus segment-B6
Glypta fumiferanae ichnovirus segment B7
Glypta fumiferanae ichnovirus segment B8
Glypta fumiferanae ichnovirus segment B9
Glypta fumiferanae ichnovirus segment C10
Glypta fumiferanae ichnovirus segment C11
Glypta fumiferanae ichnovirus segment C12
Glypta fumiferanae ichnovirus segment C13
Glypta fumiferanae ichnovirus segment C14
Glypta fumiferanae ichnovirus segment C15
Glypta fumiferanae ichnovirus segment C16
Glypta fumiferanae ichnovirus segment C17
Glypta fumiferanae ichnovirus segment C18
Glypta fumiferanae ichnovirus segment C19
Glypta fumiferanae ichnovirus segment-C1
Glypta fumiferanae ichnovirus segment C20
Glypta fumiferanae ichnovirus segment C21
Glypta fumiferanae ichnovirus segment C22
Glypta fumiferanae ichnovirus segment-C2
Glypta fumiferanae ichnovirus segment C3
Glypta fumiferanae ichnovirus segment C4
Glypta fumiferanae ichnovirus segment C5
Glypta fumiferanae ichnovirus segment C6
Glypta fumiferanae ichnovirus segment C7
Glypta fumiferanae ichnovirus segment C8
Glypta fumiferanae ichnovirus segment C9
Glypta fumiferanae ichnovirus segment D1
Glypta fumiferanae ichnovirus segment D2
Glypta fumiferanae ichnovirus segment D3
Glypta fumiferanae ichnovirus segment D4
Glypta fumiferanae ichnovirus segment D5
Glypta fumiferanae ichnovirus segment D6
Glypta fumiferanae ichnovirus segment D7
Glypta fumiferanae ichnovirus segment E1
Goatpox virus Pellor Goose circovirus
Goose hemorrhagic polyomavirus
Goose parvovirus
Gossypium darwinii symptomless alphasatellite DNA-alpha
Gossypium darwinii symptomless virus DNA-A
Gossypium davidsonii symptomless alphasatellite DNA-alpha-B
Gossypium mustilinum symptomless alphasatellite DNA-alpha-B
Gossypium punctatum mild leaf curl virus DNA A
Gossypium punctatum mild leaf curl virus DNA B
Ground squirrel hepatitis virus
Gryllus bimaculatus nudivirus Gull circovirus
Haemophilus phage HP1
Haemophilus phage HP2
Haloarcula hispanica pleomorphic virus 1
Haloarcula phage SH1
Halomonas phage phiHAP-1
Halorubrum phage HF2
Halorubrum pleomorphic virus 1
Halovirus HF1
Hamster polyomavirus
Helicoverpa armigera granulovirus
Helicoverpa armigera multiple nucleopolyhedrovirus
Helicoverpa armigera-NPV
Helicoverpa armigera NPV NNg1
Helicoverpa armigera nucleopolyhedrovirus G4
Helicoverpa zea SNPV
Heliothis virescens ascovirus 3e
Hepatitis B virus
Heron hepatitis B virus
His1 virus
His2 virus
Hollyhock leaf crumple virus
Honeysuckle yellow vein beta-JapanFukui2001
Honeysuckle yellow vein mosaic beta-JapanMiyizaki2001
Honeysuckle yellow vein mosaic disease associated satellite DNA beta-Ibaraki
Honeysuckle yellow vein mosaic Virus
Honeysuckle yellow vein mosaic virus-Kagoshima
Honeysuckle yellow vein mosaic virus satellite DNA beta
Honeysuckle yellow vein virus-UK1
Horsegram yellow mosaic Virus DNA B
Horsegram yellow mosaic virus
Horseradish curly top virus
Human adenovirus 54
Human adenovirus A
Human adenovirus B1
Human adenovirus B2
Human adenovirus C
Human adenovirus D
Human adenovirus E
Human adenovirus F
Human bocavirus 1
Human bocavirus 2
Human bocavirus 3
Human bocavirus 4
Human erythrovirus V9
Human herpesvirus 1
Human herpesvirus 2
Human herpesvirus 3
Human herpesvirus 4
Human herpesvirus 5 strain Merlin
Human herpesvirus 7
Human herpesvirus 8
Human papillomavirus-18
Human papillomavirus 1
Human papillomavirus-2
Human papillomavirus 54
Human papillomavirus-5
Human papillomavirus type 101
Human papillomavirus type 103
Human papillomavirus type 108
Human papillomavirus type-10
Human papillomavirus type 16
Human papillomavirus type 26
Human papillomavirus type 32
Human papillomavirus type 34
Human papillomavirus type 41
Human papillomavirus type 48
Human papillomavirus type 49
Human papillomavirus type-4
Human papillomavirus type 50
Human papillomavirus type 53
Human papillomavirus type 60
Human papillomavirus type 63
Human papillomavirus type 6b
Human papillomavirus type 7
Human papillomavirus type 88
Human papillomavirus type 90
Human papillomavirus type 92
Human papillomavirus type 96
Human papillomavirus type-9
Human parvovirus B19
Human T-lymphotropic virus 1
Human T-lymphotropic virus 4
Hyperthermophilic Archaeal Virus 1
Hyperthermophilic Archaeal Virus 2
Hyphantria cunea nucleopolyhedrovirus
Hyposoter fugitivus ichnovirus segment A1
Hyposoter fugitivus ichnovirus segment A2
Hyposoter fugitivus ichnovirus segment A3
Hyposoter fugitivus ichnovirus segment B10
Hyposoter fugitivus ichnovirus segment B11
Hyposoter fugitivus ichnovirus segment B12
Hyposoter fugitivus ichnovirus segment B13
Hyposoter fugitivus ichnovirus segment B14
Hyposoter fugitivus ichnovirus segment B15
Hyposoter fugitivus ichnovirus segment B16
Hyposoter fugitivus ichnovirus segment B17
Hyposoter fugitivus ichnovirus segment B18
Hyposoter fugitivus ichnovirus segment-B1
Hyposoter fugitivus ichnovirus segment B2
Hyposoter fugitivus ichnovirus segment B3
Hyposoter fugitivus ichnovirus segment B4
Hyposoter fugitivus ichnovirus segment B5
Hyposoter fugitivus ichnovirus segment B6
Hyposoter fugitivus ichnovirus segment B7
Hyposoter fugitivus ichnovirus segment B8
Hyposoter fugitivus ichnovirus segment B9
Hyposoter fugitivus ichnovirus segment C10
Hyposoter fugitivus ichnovirus segment C11
Hyposoter fugitivus ichnovirus segment C12
Hyposoter fugitivus ichnovirus segment C13
Hyposoter fugitivus ichnovirus segment C14
Hyposoter fugitivus ichnovirus segment C15
Hyposoter fugitivus ichnovirus segment C16
Hyposoter fugitivus ichnovirus segment C17
Hyposoter fugitivus ichnovirus segment C18
Hyposoter fugitivus ichnovirus segment C19
Hyposoter fugitivus ichnovirus segment-C1
Hyposoter fugitivus ichnovirus segment C20
Hyposoter fugitivus ichnovirus segment-C2
Hyposoter fugitivus ichnovirus segment C3
Hyposoter fugitivus ichnovirus segment C4
Hyposoter fugitivus ichnovirus segment C5
Hyposoter fugitivus ichnovirus segment C6
Hyposoter fugitivus ichnovirus segment C7
Hyposoter fugitivus ichnovirus segment C8
Hyposoter fugitivus ichnovirus segment C9
Hyposoter fugitivus ichnovirus segment D10
Hyposoter fugitivus ichnovirus segment D11
Hyposoter fugitivus ichnovirus segment D12
Hyposoter fugitivus ichnovirus segment-D1
Hyposoter fugitivus ichnovirus segment D2
Hyposoter fugitivus ichnovirus segment D3
Hyposoter fugitivus ichnovirus segment D4
Hyposoter fugitivus ichnovirus segment D5
Hyposoter fugitivus ichnovirus segment D6
Hyposoter fugitivus ichnovirus segment D7
Hyposoter fugitivus ichnovirus segment D8
Hyposoter fugitivus ichnovirus segment D9
Hyposoter fugitivus ichnovirus segment E1
Hyposoter fugitivus ichnovirus segment E2
Hyposoter fugitivus ichnovirus segment G1
Ictalurid herpesvirus 1 strain Auburn 1
Indian cassava mosaic virus DNA A
Indian cassava mosaic virus DNA B
Infectious hypodermal and hematopoietic necrosis virus
Infectious spleen and kidney necrosis virus
Invertebrate iridescent virus 6
Iodobacteriophage phiPLPE
Ipomoea yellow vein virus
Jatropha leaf curl virus DNA A
Jatropha yellow mosaic India virus DNA-A
JC polyomavirus
Junonia coenia densovirus
Kalanchoe top-spotting virus
Kenaf leaf curl virus DNA A
KI polyomavirus Stockholm 60
Klebsiella phage KP15
Klebsiella phage KP32
Klebsiella phage KP34
Klebsiella phage phiKO2
Kluyvera phage Kvp1
Kudzu mosaic virus DNA-A
Kudzu mosaic virus DNA-B
Lactobacillus johnsonii prophage Lj771
Lactobacillus phage A2
Lactobacillus phage KC5a
Lactobacillus phage Lb338-1
Lactobacillus phage Lc-Nu
Lactobacillus phage LL-H
Lactobacillus phage LP65
Lactobacillus phage Lrm1
Lactobacillus phage Lv-1
Lactobacillus phage phiAT3
Lactobacillus phage phig1e
Lactobacillus phage phiJL-1
Lactobacillus prophage Lj928
Lactobacillus prophage Lj965
Lactobacillus prophage phiadh
Lactococcus phage 1706
Lactococcus phage 4268
Lactococcus phage 712
Lactococcus phage asccphi28
Lactococcus phage bIBB29
Lactococcus phage bIL170
Lactococcus phage bIL67
Lactococcus phage BK5-T
Lactococcus phage c2
Lactococcus phage jj50
Lactococcus phage KSY1
Lactococcus phage P008
Lactococcus phage P087
Lactococcus phage phiLC3
Lactococcus phage Q54
Lactococcus phage r1t
Lactococcus phage sk1
Lactococcus phage TP901-1
Lactococcus phage Tuc2009
Lactococcus phage ul36
Lactococcus prophage bIL285
Lactococcus prophage bIL286
Lactococcus prophage bIL309
Lactococcus prophage bIL310
Lactococcus prophage bIL311
Lactococcus prophage bIL312
Lamium leaf distortion associated virus
Leucania separata nuclear polyhedrosis virus
Leucas zeylanica yellow vein virus satellite DNA beta
Lindernia anagallis yellow vein virus DNA-A
Lindernia anagallis yellow vein virus satellite DNA beta
Listeria phage A006
Listeria phage A118
Listeria phage A500
Listeria phage A511
Listeria phage B025
Listeria phage B054
Listeria phage P35
Listeria phage P40
Listonella phage phiHSIC
Loofa yellow mosaic virus DNA A
Loofa yellow mosaic virus DNA B
Lucky bamboo bacilliform virus
Ludwigia leaf distortion betasatellite IndiaAmadalavalasaHibiscus2 007
Ludwigia yellow vein virus-associated DNA beta
Ludwigia yellow vein virus DNA-A
Luffa begomovirus associated DNA beta
Luffa puckering and leaf distortion-associated DNA beta
LuIII virus
Lumpy skin disease virus NI-2490
Lymantria dispar MNPV
Lymantria xylina MNPV
Lymphocystis disease virus 1
Lymphocystis disease virus-isolate China
Macacine herpesvirus 1
Macacine herpesvirus 3
Macacine herpesvirus 4
Macacine herpesvirus 5
Macaque simian foamy virus
Macroptilium golden mosaic virus-
JamaicaWissadulaAugust Town DNA A
Macroptilium golden mosaic virus-
JamaicaWissadulaAugust Town DNA B
Macroptilium mosaic Puerto Rico virus DNA A
Macroptilium mosaic Puerto Rico virus DNA B
Macroptilium yellow mosaic Florida virus DNA A
Macroptilium yellow mosaic Florida virus DNA B
Macroptilium yellow mosaic virus DNA A
Macroptilium yellow mosaic virus DNA B
Maize streak virus-ASouth Africa
Malachra yellow vein mosaic virus-associated satellite DNA beta
Mal de Rio Cuarto virus segment 9
Malvastrum leaf curl Guangdong virus
Malvastrum leaf curl virus-associated defective DNA beta
Malvastrum leaf curl virus-G87
Malvastrum yellow mosaic virus-associated DNA 1
Malvastrum yellow mosaic virus DNA-A
Malvastrum yellow mosaic virus satellite DNA beta
Malvastrum yellow vein Baoshan virus DNA-A
Malvastrum yellow vein-virus
Malvastrum yellow vein virus satellite DNA beta
Malvastrum yellow vein Yunnan-virus
Malvastrum yellow vein Yunnan virus satellite DNA beta
Mamestra configurata NPV-A
Mamestra configurata NPV-B
Mannheimia phage phiMHaA1
Maruca vitrata MNPV
Mastomys coucha papillomavirus 2
Mastomys natalensis papillomavirus
Melanoplus sanguinipes entomopoxvirus
Meleagrid herpesvirus 1
Melon chlorotic leaf curl virus DNA A
Melon chlorotic mosaic virus-associated alphasatellite
Melon chlorotic mosaic virus DNA-A
Melon chlorotic mosaic virus DNA-B
Merkel cell polyomavirus
Merremia mosaic virus DNA A
Merremia mosaic virus DNA B
Mesta yellow vein mosaic Bahraich virus-
IndiaBahraich2007 DNA A
Mesta yellow vein mosaic virus-associated DNA beta
Mesta yellow vein mosaic virus DNA-A
Methanobacterium phage psiM2
Methanothermobacter prophage psiM100
Microbacterium phage Min1
Microcystis phage Ma-LMM01
Microplitis demolitor bracovirus segment A
Microplitis demolitor bracovirus segment B
Microplitis demolitor bracovirus segment C
Microplitis demolitor bracovirus segment D
Microplitis demolitor bracovirus segment E
Microplitis demolitor bracovirus segment F
Microplitis demolitor bracovirus segment G
Microplitis demolitor bracovirus segment H
Microplitis demolitor bracovirus segment I
Microplitis demolitor bracovirus segment J
Microplitis demolitor bracovirus segment K
Microplitis demolitor bracovirus segment L
Microplitis demolitor bracovirus segment M
Microplitis demolitor bracovirus segment N
Microplitis demolitor bracovirus segment O
Milk vetch dwarf virus segment 10
Milk vetch dwarf virus segment 11
Milk vetch dwarf virus segment-1
Milk vetch dwarf virus segment 2
Milk vetch dwarf virus segment 3
Milk vetch dwarf virus segment 4
Milk vetch dwarf virus segment 5
Milk vetch dwarf virus segment 6
Milk vetch dwarf virus segment 7
Milk vetch dwarf virus segment 8
Milk vetch dwarf virus segment 9
Mimosa yellow leaf curl virus-associated DNA 1
Mimosa yellow leaf curl virus DNA-A
Mimosa yellow leaf curl virus satellite DNA beta
Minute virus of mice
Mirabilis mosaic virus
Miscanthus streak virus-91
Molluscum contagiosum virus subtype 1
Monkeypox virus Zaire-96-I-16
Morganella phage MmP1
Mouse mammary tumor virus
Mouse parvovirus 1
Mouse parvovirus 2
Mouse parvovirus 3
Mouse parvovirus 4
Mouse parvovirus 5
Mulard duck circovirus
Mungbean yellow mosaic India virus DNA A
Mungbean yellow mosaic India virus DNA B
Mungbean yellow mosaic virus DNA A
Mungbean yellow mosaic virus DNA B
Murid herpesvirus 1
Murid herpesvirus 2
Murid herpesvirus 4
Murine adenovirus 3
Murine adenovirus A
Murine pneumotropic virus
Murine polyomavirus
Murine type C retrovirus
Musca domestica salivary gland hypertrophy virus
Muscovy duck circovirus
Muscovy duck parvovirus
Mus musculus papillomavirus type 1
Mycobacterium phage 244
Mycobacterium phage Adjutor
Mycobacterium phage Angel
Mycobacterium phage angelica
Mycobacterium phage Ardmore
Mycobacterium phage Barnyard
Mycobacterium phage Bethlehem
Mycobacterium phage Boomer
Mycobacterium phage BPs
Mycobacterium phage Brujita
Mycobacterium phage Butterscotch
Mycobacterium phage Bxb1
Mycobacterium phage Bxz1
Mycobacterium phage Bxz2
Mycobacterium phage Cali
Mycobacterium phage Catera
Mycobacterium phage Chah
Mycobacterium phage Che12
Mycobacterium phage Che8
Mycobacterium phage Che9c
Mycobacterium phage Che9d
Mycobacterium phage Cjw1
Mycobacterium phage Cooper
Mycobacterium phage Corndog
Mycobacterium phage CrimD
Mycobacterium phage D29
Mycobacterium phage DD5
Mycobacterium phage ET08
Mycobacterium phage Fruitloop
Mycobacterium phage Giles
Mycobacterium phage Gumball
Mycobacterium phage Halo
Mycobacterium phage Jasper
Mycobacterium phage KBG
Mycobacterium phage Konstantine
Mycobacterium phage Kostya
Mycobacterium phage L5
Mycobacterium phage LeBron
Mycobacterium phage Llij
Mycobacterium phage Lockley
Mycobacterium phage Myrna
Mycobacterium phage Nigel
Mycobacterium phage Omega
Mycobacterium phage Orion
Mycobacterium phage Pacc40
Mycobacterium phage PBI1
Mycobacterium phage Peaches
Mycobacterium phage PG1
Mycobacterium phage Phaedrus
Mycobacterium phage Phlyer
Mycobacterium phage Pipefish
Mycobacterium phage Plot
Mycobacterium phage PMC
Mycobacterium phage Porky
Mycobacterium phage Predator
Mycobacterium phage Pukovnik
Mycobacterium phage Qyrzula
Mycobacterium phage Ramsey
Mycobacterium phage Rizal
Mycobacterium phage Rosebush
Mycobacterium phage ScottMcG
Mycobacterium phage Solon
Mycobacterium phage Spud
Mycobacterium phage TM4
Mycobacterium phage Troll4
Mycobacterium phage Tweety
Mycobacterium phage U2
Mycobacterium phage Wildcat
Mycoplasma phage MAV1
Mycoplasma phage P1
Mycoplasma phage phiMFV1
Myotis polyomavirus VM-2008
Mythimna loreyi densovirus
Myxococcus phage Mx8
Myxoma virus
Myzus persicae densovirus
Nanovirus-like particle
Natrialba phage PhiCh1
Neodiprion abietis NPV
Neodiprion lecontei NPV
Neodiprion sertifer NPV Oat dwarf virus
OkLCV satDNA 10
Okra leaf curl disease associated DNA 1
Okra leaf curl Mali virus satellite DNA beta
Okra leaf curl virus-Cameroon
Okra mottle virus-Brazilokra DNA A
Okra mottle virus-Brazilokra DNA B
Okra yellow crinkle virus segment A
Okra yellow mosaic Mexico virus DNA A
Okra yellow mosaic Mexico virus DNA B
Okra yellow vein disease associated sequence virion
Okra yellow vein mosaic virus
Old World harvest mouse papillomavirus
Orangutan polyomavirus Orf virus
Orgyia leucostigma NPV
Orgyia pseudotsugata MNPV
Oryctes rhinoceros virus
Ostreid herpesvirus 1
Ostreococcus tauri virus 1
Ostreococcus virus OsV5
Ovine adenovirus A
Ovine adenovirus D
Ovine herpesvirus 2
Ovine papillomavirus-1
Panicum streak virus-Karino
Panine herpesvirus 2 strain Heberling
Papaya leaf curl China virus-G8
Papaya leaf curl China virus satellite DNA beta
Papaya leaf curl Guandong virus-GD2 DNA A
Papaya leaf curl virus-associated DNA beta
Papaya leaf curl-virus Papiine herpesvirus 2
Paramecium bursaria Chlorella virus 1
Paramecium bursaria Chlorella virus AR158
Paramecium bursaria Chlorella virus FR483
Paramecium bursaria Chlorella virus NY2A
Parvovirus H1
Passionfruit severe leaf distortion virus DNA-A
Passionfruit severe leaf distortion virus DNA-B
Pasteurella phage F108
Peanut chlorotic streak virus
Pedilanthus leaf curl virus-
Pedilanthus PakistanMultan2004
Pelargonium vein banding virus
Penaeus merguiensis densovirus
Penaeus monodon hepatopancreatic parvovirus
Pepper curly top virus
Pepper golden mosaic virus DNA A
Pepper golden mosaic virus DNA B
Pepper huasteco yellow vein virus DNA A
Pepper huasteco yellow vein virus DNA B
Pepper leaf curl Bangladesh virus segment A component
Pepper leaf curl virus DNA-A
Pepper leaf curl virus satellite DNA beta
Pepper leaf curl Yunnan virus satellite DNA beta
Pepper leaf curl Yunnan virus-YN323
Pepper yellow dwarf virus-New Mexico
Pepper yellow leaf curl Indonesia virus DNA-A
Pepper yellow leaf curl Indonesia virus DNA-B
Pepper yellow vein Mali virus
Periplaneta fuliginosa densovirus
Petunia vein clearing virus
Phage cdtI
Phage Gifsy-1
Phage Gifsy-2
Phage phiJL001
Phocoena spinipinnis papillomavirus
Phormidium phage Pf-WMP3
Phormidium phage Pf-WMP4
Phthorimaea operculella granulovirus
Pieris rapae granulovirus
Planaria asexual strain-specific virus-like element type 1 large DNA segment
Planaria asexual strain-specific virus-like element type 1 small DNA segment
Planococcus citri densovirus
Plutella xylostella granulovirus
Plutella xylostella multiple nucleopolyhedrovirus
Polyomavirus HPyV6
Polyomavirus HPyV7
Porcine adenovirus C
Porcine circovirus 1
Porcine circovirus 2
Porcine endogenous retrovirus E
Porcine parvovirus
Potato apical leaf curl disease-associated satellite DNA beta
Potato yellow mosaic
Panama virus DNA A
Potato yellow mosaic
Panama virus DNA B
Potato yellow mosaic Trinidad virus DNA A
Potato yellow mosaic Trinidad virus DNA B
Potato yellow mosaic virus DNA A
Potato yellow mosaic virus DNA B
Prochlorococcus phage P-SSM4
Propionibacterium phage B5
Propionibacterium phage PA6
Pseudaletia unipuncta granulovirus
Pseudoalteromonas phage PM2
Pseudocowpox virus
Pseudomonas phage 119X
Pseudomonas phage 14-1
Pseudomonas phage 201phi2-1
Pseudomonas phage 73
Pseudomonas phage B3
Pseudomonas phage D3112
Pseudomonas phage-D3
Pseudomonas phage DMS3
Pseudomonas phage EL
Pseudomonas phage F10
Pseudomonas phage F116
Pseudomonas phage F8
Pseudomonas phage gh-1
Pseudomonas phage LBL3
Pseudomonas phage LIT1
Pseudomonas phage LKD16
Pseudomonas phage LMA2
Pseudomonas phage LUZ19
Pseudomonas phage LUZ24
Pseudomonas phage LUZ7
Pseudomonas phage M6
Pseudomonas phage MP22
Pseudomonas phage MP29
Pseudomonas phage MP38
Pseudomonas phage PA11
Pseudomonas phage PAJU2
Pseudomonas phage PaP2
Pseudomonas phage PaP3
Pseudomonas phage PB1
Pseudomonas phage Pf1
Pseudomonas phage Pf3
Pseudomonas phage phi-2
Pseudomonas phage phiCTX
Pseudomonas phage phikF77
Pseudomonas phage phiKMV
Pseudomonas phage phiKZ
Pseudomonas phage PT2
Pseudomonas phage PT5
Pseudomonas phage SN
Pseudomonas phage YuA
Psittacid herpesvirus 1
Psittacus erithacus timneh papillomavirus
Pumpkin yellow mosaic Malaysia virus DNA A
Pyrobaculum spherical virus
Pyrococcus abyssi virus 1
Rabbit fibroma virus
Rabbit oral papillomavirus
Rachiplusia ou MNPV
Radish leaf curl virus satellite DNA beta
Radish leaf curl virus segment A
Ralstonia phage p12J
Ralstonia phage phiRSA1
Ralstonia phage RSB1
Ralstonia phage RSL1
Ralstonia phage RSM1
Ralstonia phage RSM3
Ralstonia phage RSS1
Ramie mosaic virus DNA-A
Ramie mosaic virus DNA-B
Ranid herpesvirus 1 strain McKinnell
Ranid herpesvirus 2 strain ATCC VR-568
Rauscher murine leukemia virus
Raven circovirus RD114 retrovirus
Reticuloendotheliosis virus
Rhesus monkey
Papillomavirus
Rhizobium phage 16-3
Rhodothermus phage RM378
Rhynchosia golden mosaic virus DNA A
Rhynchosia golden mosaic virus DNA B
Rhynchosia golden mosaic Yucatan virus DNA A
Rhynchosia golden mosaic Yucatan virus DNA B
Rice tungro bacilliform virus
Roseobacter phage SIO1
Roseophage DSS3P2
Roseophage EE36P1
Rosss goose hepatitis B virus
Rousettus aegyptiacus papillomavirus type 1
Rudbeckia flower distortion virus
Saccharum streak virus
Saimiriine herpesvirus 2
Salmonella enterica bacteriophage SE1
Salmonella phage c341
Salmonella phage E1
Salmonella phage epsilon34
Salmonella phage Fels-1
Salmonella phage phiSG-JL2
Salmonella phage SETP3
Salmonella phage ST64B
Sclerotinia sclerotiorum hypovirulence associated DNA virus 1
Sea turtle tornovirus 1
Senecio yellow mosaic virus
Sheeppox virus 17077-99
Sheldgoose hepatitis B virus
Shigella phage phiSboM-AG3
Shrimp white spot syndrome virus
Sida golden mosaic Costa Rica virus DNA A
Sida golden mosaic Costa Rica virus DNA B
Sida golden mosaic Florida virus-Malvastrum DNA-A
Sida golden mosaic Florida virus-Malvastrum DNA-B
Sida golden mosaic Honduras virus DNA A
Sida golden mosaic Honduras virus DNA B
Sida golden mosaic virus DNA-A
Sida golden mosaic virus DNA-B
Sida golden mottle virus DNA-A
Sida golden mottle virus DNA-B
Sida leaf curl virus-associated DNA 1
Sida leaf curl virus-associated DNA beta
Sida leaf curl-virus
Sida leaf curl virus satellite DNA beta
Sida micrantha mosaic virus segment A
Sida micrantha mosaic virus segment B
Sida mosaic Sinaloa virus DNA A
Sida mosaic Sinaloa virus DNA B
Sida mottle virus
Sida yellow mosaic virus-China-associated DNA beta DNA beta
Sida yellow mosaic-virus
Sida yellow mosaic Yucatan virus DNA A
Sida yellow mosaic Yucatan virus DNA B
Sida yellow vein disease associated DNA 1
Sida yellow vein Madurai virus
Sida yellow vein Vietnam virus-associated DNA 1
Sida yellow vein Vietnam virus DNA-A
Sida yellow vein Vietnam virus satellite DNA beta
Sida yellow vein virus DNA A
Sida yellow vein virus DNA B
Sida yellow vein virus satellite DNA beta
Siegesbeckia yellow vein Guangxi virus
Siegesbeckia yellow vein virus-GD13-associated DNA beta
Siegesbeckia yellow vein virus GD13
Simian adenovirus 1
Simian adenovirus 3
Simian foamy virus 3
Simian immunodeficiency virus SIV-mnd 2
Simian retrovirus 4
Simian T-cell lymphotropic virus 6
Simian T-lymphotropic virus 1
Simian T-lymphotropic virus 3
Simian virus 40
Singapore grouper iridovirus
Sinorhizobium phage PBC5
Small anellovirus 1
Small anellovirus 2
Snake parvovirus 1
Snow goose hepatitis B virus
Sodalis phage phiSG1
Sodalis phage SO-1
South African cassava mosaic virus DNA A
South African cassava mosaic virus DNA B
Soybean chlorotic blotch virus DNA A
Soybean chlorotic blotch virus DNA B
Soybean chlorotic mottle virus
Soybean crinkle leaf virus
Soybean mild mottle virus
Spilanthes yellow vein virus DNA-A
Spinach curly top virus
Spiroplasma kunkelii virus
SkV1 CR2-3x
Spiroplasma phage 1-C74
Spiroplasma phage 1-R8A2B
Spiroplasma phage 4
Spiroplasma phage SVTS2
Spodoptera exigua MNPV
Spodoptera frugiperda ascovirus 1a
Spodoptera frugiperda MNPV virus
Spodoptera litura granulovirus
Spodoptera litura NPV
Spodoptera litura nucleopolyhedrovirus II
Sputnik virophage
Squash leaf curl China virus-B DNA-A
Squash leaf curl China virus-B DNA B
Squash leaf curl Philippines virus segment A
Squash leaf curl Philippines virus segment B
Squash leaf curl virus A component DNA
Squash leaf curl virus B component DNA
Squash leaf curl Yunnan virus
Squash mild leaf curl virus-Imperial Valley DNA A
Squash mild leaf curl virus-Imperial Valley DNA B
Squash yellow mild mottle virus DNA B
Squirrel monkey polyomavirus
Sri Lankan cassava mosaic virus DNA A
Sri Lankan cassava mosaic virus DNA B
Stachytarpheta leaf curl virus
Staphylococcus phage 11
Staphylococcus phage 187
Staphylococcus phage 2638A
Staphylococcus phage 29
Staphylococcus phage 37
Staphylococcus phage 3A
Staphylococcus phage 42e
Staphylococcus phage 44AHJD
Staphylococcus phage 47
Staphylococcus phage 52A
Staphylococcus phage 53
Staphylococcus phage 55
Staphylococcus phage 66
Staphylococcus phage 69
Staphylococcus phage 71
Staphylococcus phage 77
Staphylococcus phage 80alpha
Staphylococcus phage 85
Staphylococcus phage 88
Staphylococcus phage 92
Staphylococcus phage 96
Staphylococcus phage CNPH82
Staphylococcus phage EW
Staphylococcus phage G1
Staphylococcus phage K
Staphylococcus phage P954
Staphylococcus phage PH15
Staphylococcus phage phi2958PVL
Staphylococcus phage phiETA2
Staphylococcus phage phiETA3
Staphylococcus phage-phiETA
Staphylococcus phage phiMR11
Staphylococcus phage phiMR25
Staphylococcus phage phiNM1
Staphylococcus phage phiNM3
Staphylococcus phage phiP68
Staphylococcus phage phiPVL108
Staphylococcus phage phiPVL-CN125
Staphylococcus phage phiSauS-IPLA35
Staphylococcus phage phiSauS-IPLA88
Staphylococcus phage phiSLT
Staphylococcus phage PT1028
Staphylococcus phage ROSA
Staphylococcus phage SAP-26
Staphylococcus phage SAP2
Staphylococcus phage Twort
Staphylococcus phage X2
Staphylococcus prophage phi 12
Staphylococcus prophage phi 13
Staphylococcus prophage phiN315
Staphylococcus prophage phiPV83
Staphylococcus prophage PVL
Staphylococcus prophage tp310-1
Staphylococcus prophage tp310-2
Staphylococcus prophage tp310-3
Starling circovirus
Stenotrophomonas phage phiSMA9
Stenotrophomonas phage S1
Strawberry vein banding virus
Streptococcus phage 2972
Streptococcus phage 5093
Streptococcus phage 7201
Streptococcus phage 858
Streptococcus phage Abc2
Streptococcus phage ALQ13.2
Streptococcus phage C1
Streptococcus phage Cp-1
Streptococcus phage DT1
Streptococcus phage M102
Streptococcus phage O1205
Streptococcus phage P9
Streptococcus phage PH10
Streptococcus phage PH15
Streptococcus phage phi3396
Streptococcus phage Sfi11
Streptococcus phage Sfi19
Streptococcus phage Sfi21
Streptococcus phage SM1
Streptococcus phage SMP
Streptococcus prophage 315.1
Streptococcus prophage 315.2
Streptococcus prophage 315.5
Streptococcus prophage 315.6
Streptococcus prophage EJ-1
Streptococcus prophage MM1
Streptococcus pyogenes phage 315.3
Streptomyces phage mu16
Streptomyces phage phiBT1
Streptomyces phage phiC31
Streptomyces phage phiSASD1
Streptomyces phage VWB Stx1 converting phage
Stx2-converting phage 1717
Stx2-converting phage 86
Stx2 converting phage-I
Stx2 converting phage II
Subterranean clover stunt virus DNA 1
Subterranean clover stunt virus DNA 2
Subterranean clover stunt virus DNA 3
Subterranean clover stunt virus DNA 4
Subterranean clover stunt virus DNA 5
Subterranean clover stunt virus DNA 6
Subterranean clover stunt virus DNA 7
Subterranean clover stunt virus DNA 8
Sugarcane bacilliform IM virus
Sugarcane bacilliform Mor virus
Sugarcane bacilliform virus
Sugarcane streak Egypt virus-Giza
Sugarcane streak Reunion virus
Sugarcane streak virus-Natal
Suid herpesvirus 1
Sulfolobus islandicus filamentous virus
Sulfolobus islandicus rod-shaped virus 1
Sulfolobus islandicus rod-shaped virus 2
Sulfolobus spindle-shaped virus 4
Sulfolobus spindle-shaped virus 5
Sulfolobus spindle-shaped virus 6
Sulfolobus spindle-shaped virus 7
Sulfolobus turreted icosahedral virus 2
Sulfolobus turreted icosahedral-virus
Sulfolobus virus 1
Sulfolobus virus 2
Sulfolobus virus Kamchatka 1
Sulfolobus virus Ragged Hills
Sulfolobus virus STSV1
Sunn hemp leaf distortion virus DNA-A
Sus scrofa papillomavirus type 1
Sweetpotato badnavirus B
Sweet potato leaf curl Bengal virus-IndiaWest Bengal2008 segment A
Sweet potato leaf curl Canary virus
Sweet potato leaf curl Georgia virus
Sweet potato leaf curl Lanzarote virus
Sweet potato leaf curl Spain virus
Sweet potato leaf curl virus
Swinepox virus Synechococcus phage P60
Synechococcus phage S-PM2
Synechococcus phage S-RSM4
Synechococcus phage syn9
Tanapox virus
Taro bacilliform virus
Taterapox virus
Thalassomonas phage BA3
Thermoproteus tenax spherical virus 1
Thermus phage IN93
Thermus phage P23-45
Thermus phage P23-77
Thermus phage P74-26
Thermus phage phiYS40
Tobacco curly shoot virus associated DNA 1
Tobacco curly shoot virus-associated DNA beta
Tobacco curly shoot-virus
Tobacco leaf curl disease associated sequence virion
Tobacco leaf curl Japan virus
Tobacco leaf curl Kochi virus
Tobacco leaf curl Thailand virus
Tobacco leaf curl virus-associated DNA beta
Tobacco leaf curl Yunnan virus associated DNA 1
Tobacco leaf curl Yunnan virus satellite DNA beta
Tobacco leaf curl Yunnan virus-Y136
Tobacco leaf curl Zimbabwe virus
Tobacco vein clearing virus
Tobacco yellow dwarf virus
Tomato begomovirus satellite DNA beta
Tomato chino La Paz virus segment A
Tomato chlorotic mottle virus DNA A
Tomato chlorotic mottle virus DNA B
Tomato common mosaic virus DNA-A
Tomato common mosaic virus DNA-B
Tomato curly stunt virus
Tomato golden mosaic virus DNA A
Tomato golden mosaic virus DNA B
Tomato golden mottle virus DNA A
Tomato golden mottle virus DNA B
Tomato leaf curl Arusha virus DNA-A
Tomato leaf curl Bangalore virus-Ban5 satellite DNA beta
Tomato leaf curl Bangalore-virus
Tomato leaf curl Bangladesh virus
Tomato leaf curl Cameroon virus-CameroonBueaOkra2008
Tomato leaf curl Cebu virus DNA-A
Tomato leaf curl China virus-G32
Tomato leaf curl Cotabato virus DNA-A
Tomato leaf curl Ghana virus segment A
Tomato leaf curl Guangdong virus DNA-A
Tomato leaf curl Guangxi virus
Tomato leaf curl Gujarat virus-Varanasi segment A
Tomato leaf curl Gujarat virus-Varanasi segment B
Tomato leaf curl Hainan virus
Tomato leaf curl Hsinchu virus-TaiwanHsinchu2005 DNA A
Tomato leaf curl Iran virus
Tomato leaf curl Java virus-Ageratum satellite DNA
Tomato leaf curl Java-virus
Tomato leaf curl Joydebpur beta virus
Tomato leaf curl Joydebpur virus DNA-A
Tomato leaf curl Karnataka virus-associated DNA beta DNA-A
Tomato leaf curl Karnataka-virus
Tomato leaf curl Kerala virus
Tomato leaf curl Kumasi virus segment A
Tomato leaf curl Laos virus
Tomato leaf curl Malaysia virus
Tomato leaf curl Mali virus
Tomato leaf curl Mayotte virus
Tomato leaf curl Mindanao virus DNA-A
Tomato leaf curl New Delhi virus-associated DNA beta
Tomato leaf curl New Delhi virus DNA A
Tomato leaf curl New Delhi virus DNA B
Tomato leaf curl Nigeria virus-Nigeria2006
Tomato leaf curl Pakistan virus associated DNA 1
Tomato leaf curl Pakistan virus segment A
Tomato leaf curl Palampur virus
Tomato leaf curl Patna virus DNA-A
Tomato leaf curl Philippines virus
Tomato leaf curl Philippine virus satellite DNA beta
Tomato leaf curl Pune virus
Tomato leaf curl Seychelles virus
Tomato leaf curl Sinaloa virus DNA A
Tomato leaf curl Sinaloa virus DNA B
Tomato leaf curl Sri Lanka virus
Tomato leaf curl Sudan virus-Gezira
Tomato leaf curl Sulawesi virus DNA-A
Tomato leaf curl Taiwan virus
Tomato leaf curl Togo virus-Togo2006
Tomato leaf curl Vietnam virus DNA A
Tomato leaf curl virus-associated DNA beta
Tomato leaf curl-virus
Tomato leaf curl virus-Pune-associated DNA beta DNA-A
Tomato mild mosaic virus DNA-A
Tomato mild mosaic virus DNA-B
Tomato mild yellow leaf curl Aragua virus DNA A
Tomato mild yellow leaf curl Aragua virus DNA B
Tomato mosaic Havana virus DNA A
Tomato mosaic Havana virus DNA B
Tomato mosaic leaf curl virus DNA A
Tomato mosaic leaf curl virus DNA B
Tomato mottle Taino virus DNA A
Tomato mottle Taino virus DNA B
Tomato mottle virus DNA A
Tomato mottle virus DNA B
Tomato pseudo-curly top virus
Tomato rugose mosaic virus DNA A
Tomato rugose mosaic virus DNA B
Tomato severe leaf curl virus
Tomato severe rugose virus DNA A
Tomato severe rugose virus DNA B
Tomato yellow dwarf disease associated satellite DNA beta-Kochi virus
Tomato yellow leaf curl China virus associated DNA 1
Tomato yellow leaf curl China-virus
Tomato yellow leaf curl Guangdong virus DNA-A
Tomato yellow leaf curl Indonesia virus-Lembang
Tomato yellow leaf curl Kanchanaburi virus DNA A
Tomato yellow leaf curl Kanchanaburi virus DNA B
Tomato yellow leaf curl Mali virus-associated DNA beta
Tomato yellow leaf curl Thailand virus associated DNA 1
Tomato yellow leaf curl Thailand virus DNA A
Tomato yellow leaf curl Thailand virus DNA B
Tomato yellow leaf curl Vietnam virus DNA-A
Tomato yellow leaf curl Vietnam virus satellite DNA beta
Tomato yellow leaf curl virus-associated DNA beta
Tomato yellow margin leaf curl virus DNA A
Tomato yellow margin leaf curl virus DNA B
Tomato yellow spot virus DNA-A
Tomato yellow spot virus DNA-B
Tomato yellow vein streak virus DNA-A
Tomato yellow vein streak virus DNA-B
Torque teno canis virus Torque teno douroucouli virus
Torque teno felis virus
Torque teno midi virus 1
Torque teno midi virus 2
Torque teno mini virus 1
Torque teno mini virus 2
Torque teno mini virus 3
Torque teno mini virus 4
Torque teno mini virus 5
Torque teno mini virus 6
Torque teno mini virus 7
Torque teno mini virus 8
Torque teno mini virus 9
Torque teno sus virus 1
Torque teno tamarin virus
Torque teno virus 10
Torque teno virus 12
Torque teno virus 14
Torque teno virus 15
Torque teno virus 16
Torque teno virus 19
Torque teno virus-1
Torque teno virus 25
Torque teno virus 26
Torque teno virus 27
Torque teno virus 28
Torque teno virus 3
Torque teno virus 4
Torque teno virus 6
Torque teno virus 7
Torque teno virus 8
Trichodysplasia spinulosa-associated polyomavirus
Trichoplusia ni ascovirus 2c
Trichoplusia ni SNPV
Tupaiid herpesvirus 1
Turkey adenovirus A
Turnip curly top virus
TYLCCNV-Y322 satellite DNA beta
Urochloa streak virus Vaccinia virus Variola virus
Velvet bean severe mosaic virus DNA A
Velvet bean severe mosaic virus DNA B
Vernonia yellow vein betasatellite
Vernonia yellow vein virus DNA-A
Vibrio phage fs1
Vibrio phage fs2
Vibrio phage K139
Vibrio phage kappa
Vibrio phage KSF-1phi
Vibrio phage KVP40
Vibrio phage N4
Vibrio phage VEJphi
Vibrio phage Vf12
Vibrio phage VfO3K6
Vibrio phage VfO4K68
Vibrio phage VGJphi
Vibrio phage VHML
Vibrio phage VP2
Vibriophage VP4
Vibrio phage VP5
Vibrio phage VP882
Vibrio phage VP93
Vibrio phage VpV262
Vibrio phage VSK
Watermelon chlorotic stunt virus DNA A
Watermelon chlorotic stunt virus DNA B
Wheat dwarf virus
Wissadula golden mosaic St Thomas Virus DNA A
Wissadula golden mosaic St Thomas Virus DNA B
Woodchuck hepatitis virus
WU Polyomavirus
Xanthomonas phage Cf1c
Xanthomonas phage OP1
Xanthomonas phage OP2
Xanthomonas phage phiL7
Xanthomonas phage Xop411
Xanthomonas phage Xp10
Xanthomonas phage Xp15
Xenopus laevis endogenous retrovirus Xen1
Xestia c-nigrum granulovirus
Xylella phage Xfas53
Yaba-like disease virus
Yaba monkey tumor virus
Yersinia pestis phage phiA1122
Yersinia phage Berlin
Yersinia phage L-413C
Yersinia phage phiYeO3-12
Yersinia phage PY54
Zinnia leaf curl disease associated sequence virion
Zinnia leaf curl virus-associated DNA beta
Appendix 3: Bacterial Database
Acaryochloris marina MBIC11017
Acetobacter pasteurianus IFO 3283 01
Acetohalobium arabaticum DSM 5501
Acholeplasma laidlawii PG 8A
Achromobacter xylosoxidans A8
Acidaminococcus fermentans DSM 20731
Acidaminococcus intestini RyC MR95
Acidianus hospitalis W1
Acidilobus saccharovorans 345 15
Acidimicrobium ferrooxidans DSM 10331
Acidiphilium cryptum JF 5
Acidiphilium multivorum AIU301
Acidithiobacillus caldus SM 1
Acidithiobacillus ferrivorans SS3
Acidithiobacillus ferrooxidans ATCC 23270
Acidobacterium capsulatum ATCC 51196
Acidothermus cellulolyticus 11B
Acidovorax avenae subsp avenae ATCC 19860
Acidovorax citrulli AAC00 1
Acidovorax ebreus TPSY
Acidovorax sp JS42
Aciduliprofundum boonei T469
Acinetobacter baumannii 1656 2
Acinetobacter calcoaceticus PHEA 2
Acinetobacter oleivorans DR1
Acinetobacter sp ADP1
Actinobacillus pleuropneumoniae serovar 5b str L20
Actinobacillus succinogenes 130Z
Actinoplanes sp SE50 110
Actinosynnema mirum DSM 43827
Aerococcus urinae ACS 120 V Col10a
Aeromonas hydrophila subsp hydrophila ATCC 7966
Aeromonas salmonicida subsp salmonicida A449
Aeromonas veronii B565
Aeropyrum pernix K1
Aggregatibacter actinomycetemcomitans D11S 1
Aggregatibacter aphrophilus NJ8700
Agrobacterium fabrum str C58
Agrobacterium radiobacter K84
Agrobacterium sp H13 3
Agrobacterium vitis S4
Akkermansia muciniphila ATCC BAA 835
Alcanivorax borkumensis SK2
Alicycliphilus denitrificans BC
Alicyclobacillus acidocaldarius subsp acidocaldarius DSM 446
Aliivibrio salmonicida LFI1238
Alkalilimnicola ehrlichii MLHE 1
Alkaliphilus metalliredigens QYMF
Alkaliphilus oremlandii OhILAs
Allochromatium vinosum DSM 180
Alteromonas macleodii str Deep ecotype
Alteromonas sp SN2
Aminobacterium colombiense DSM 12261
Ammonifex degensii KC4
Amycolatopsis mediterranei U32
Amycolicicoccus subflavus DQS3 9A1
Anabaena variabilis ATCC 29413
Anaerococcus prevotii DSM 20548
Anaerolinea thermophila UNI 1
Anaeromyxobacter dehalogenans 2CP 1
Anaeromyxobacter sp Fw109 5
Anaplasma centrale str Israel
Anaplasma marginale str Florida
Anaplasma phagocytophilum HZ
Anoxybacillus flavithermus WK1
Aquifex aeolicus VF5
Arcanobacterium haemolyticum DSM 20595
Archaeoglobus fulgidus DSM 4304
Archaeoglobus profundus DSM 5631
Archaeoglobus veneficus SNP6
Arcobacter butzleri RM4018
Arcobacter nitrofigilis DSM 7299
Arcobacter sp L
Aromatoleum aromaticum EbN1
Arthrobacter arilaitensis Re117
Arthrobacter aurescens TC1
Arthrobacter chlorophenolicus A6
Arthrobacter phenanthrenivorans Sphe3
Arthrobacter sp FB24
Aster yellows witches broom phytoplasma AYWB
Asticcacaulis excentricus CB 48
Atopobium parvulum DSM 20469
Azoarcus sp BH72
Azorhizobium caulinodans ORS 571
Azospirillum sp B510
Azotobacter vinelandii DJ Bacillus amyloliquefaciens DSM 7
Bacillus anthracis str Ames
Bacillus atrophaeus 1942
Bacillus cellulosilyticus DSM 2522
Bacillus cereus 03BB102
Bacillus clausii KSM K16
Bacillus coagulans 2 6
Bacillus cytotoxicus NVH 391 98
Bacillus halodurans C 125
Bacillus licheniformis DSM 13 ATCC 14580
Bacillus megaterium DSM 319
Bacillus mycoides DSM 2048
Bacillus pseudofirmus OF4
Bacillus pumilus SAFR 032
Bacillus selenitireducens MLS10
Bacillus subtilis BSn5
Bacillus thuringiensis serovar berliner ATCC 10792
Bacillus weihenstephanensis KBAB4
Bacteriovorax marinus SJ
Bacteroides fragilis YCH46
Bacteroides helcogenes P 36 108
Bacteroides salanitronis DSM 18170
Bacteroides thetaiotaomicron VPI 5482
Bacteroides vulgatus ATCC 8482
Bartonella bacilliformis KC583
Bartonella clarridgeiae 73
Bartonella grahamii as4aup
Bartonella henselae str Houston 1
Bartonella quintana str Toulouse
Bartonella tribocorum CIP 105476
Baumannia cicadellinicola str Hc Homalodisca coagulata
Bdellovibrio bacteriovorus HD100
Beijerinckia indica subsp indica ATCC 9039
Beutenbergia cavernae DSM 12333
Bifidobacterium adolescentis ATCC 15703
Bifidobacterium animalis subsp animalis ATCC 25527
Bifidobacterium bifidum S17
Bifidobacterium breve ACS 071 V Sch8b
Bifidobacterium dentium Bd1
Bifidobacterium longum DJO10A
Blattabacterium sp
Blattella germanica str Bge
Bordetella avium 197N
Bordetella bronchiseptica RB50
Bordetella parapertussis 12822
Bordetella pertussis CS
Bordetella petrii DSM 12804
Borrelia afzelii PKo
Borrelia bissettii DN127
Borrelia burgdorferi B31
Borrelia duttonii Ly
Borrelia garinii PBi
Borrelia hermsii DAH
Borrelia recurrentis A1
Borrelia turicatae 91E135
Brachybacterium faecium DSM 4810
Brachyspira hyodysenteriae WA1
Brachyspira intermedia PWS A
Brachyspira murdochii DSM 12563
Brachyspira pilosicoli 95 1000
Bradyrhizobium japonicum USDA 110
Bradyrhizobium sp BTAi1
Brevibacillus brevis NBRC 100599
Brevundimonas subvibrioides ATCC 15264
Brucella abortus A13334
Brucella canis ATCC 23365
Brucella melitensis bv 1 str 16M
Brucella microti CCM 4915
Brucella ovis ATCC 25840
Brucella pinnipedialis B2 94
Brucella suis 1330
Buchnera aphidicola str APS Acyrthosiphon pisum
Burkholderia ambifaria AMMD
Burkholderia cenocepacia HI2424
Burkholderia gladioli BSR3
Burkholderia glumae BGR1
Burkholderia mallei ATCC 23344
Burkholderia multivorans ATCC 17616
Burkholderia phymatum STM815
Burkholderia phytofirmans PsJN
Burkholderia pseudomallei 668
Burkholderia rhizoxinica HKI 454
Burkholderia sp 383
Burkholderia thailandensis E264
Burkholderia vietnamiensis G4
Burkholderia xenovorans LB400
Butyrivibrio proteoclasticus B316
Caldicellulosiruptor bescii DSM 6725
Caldicellulosiruptor hydrothermalis 108
Caldicellulosiruptor kristjanssonii 177R1B
Caldicellulosiruptor kronotskyensis 2002
Caldicellulosiruptor lactoaceticus 6A
Caldicellulosiruptor obsidiansis OB47
Caldicellulosiruptor owensensis OL
Caldicellulosiruptor saccharolyticus DSM 8903
Calditerrivibrio nitroreducens DSM 19672
Caldivirga maquilingensis IC 167
Campylobacter concisus 13826
Campylobacter curvus 52592
Campylobacter fetus subsp fetus 82 40
Campylobacter hominis ATCC BAA 381
Campylobacter jejuni subsp jejuni 81116
Campylobacter lari RM2100
Candidatus Accumulibacter phosphatis clade IIA str UW 1
Candidatus Amoebophilus asiaticus 5a2
Candidatus Arthromitus sp SFB mouse Japan
Candidatus Azobacteroides pseudotrichonymphae genomovar CFP2
Candidatus Blochmannia floridanus
Candidatus Carsonella ruddii PV
Candidatus Chloracidobacterium thermophilum B
Candidatus Desulforudis audaxviator MP104C
Candidatus Hamiltonella defensa 5AT Acyrthosiphon pisum
Candidatus Hodgkinia cicadicola Dsem
Candidatus Korarchaeum cryptofilum OPF8
Candidatus Koribacter versatilis Ellin345
Candidatus Liberibacter asiaticus str psy62
Candidatus Methylomirabilis oxyfera
Candidatus Midichloria mitochondrii IricVA
Candidatus Moranella endobia PCIT
Candidatus Nitrospira defluvii
Candidatus Pelagibacter sp IMCC9063
Candidatus Phytoplasma australiense
Candidatus Protochlamydia amoebophila UWE25
Candidatus Puniceispirillum marinum IMCC1322
Candidatus Riesia pediculicola USDA
Candidatus Ruthia magnifica str Cm
Calyptogena magnifica
Candidatus Solibacter usitatus Ellin6076
Candidatus Sulcia muelleri GWSS
Candidatus Tremblaya princeps PCIT
Candidatus Vesicomyosocius okutanii HA
Candidatus Zinderia insecticola CARI
Capnocytophaga canimorsus Cc5
Capnocytophaga ochracea DSM 7271
Carboxydothermus hydrogenoformans Z 2901
Carnobacterium sp 17 4
Catenulispora acidiphila DSM 44928
Caulobacter crescentus CB15
Caulobacter segnis ATCC 21756
Caulobacter sp K31
Cellulomonas fimi ATCC 484
Cellulomonas flavigena DSM 20109
Cellulophaga algicola DSM 14237
Cellulophaga lytica DSM 7489
Cellvibrio gilvus ATCC 13127
Cellvibrio japonicus Ueda107
Cenarchaeum symbiosum A
Chelativorans sp BNC1
Chitinophaga pinensis DSM 2588
Chlamydia muridarum Nigg
Chlamydia trachomatis 434 Bu
Chlamydophila abortus S26 3
Chlamydophila caviae GPIC
Chlamydophila felis Fe C 56
Chlamydophila pecorum E58
Chlamydophila pneumoniae CWL029
Chlamydophila psittaci 6BC
Chlorobaculum parvum NCIB 8327
Chlorobium chlorochromatii CaD3
Chlorobium limicola DSM 245
Chlorobium luteolum DSM 273
Chlorobium phaeobacteroides DSM 266
Chlorobium phaeovibrioides DSM 265
Chlorobium tepidum TLS
Chloroflexus aggregans DSM 9485
Chloroflexus aurantiacus J 10 fl
Chloroflexus sp Y 400 fl
Chloroherpeton thalassium ATCC 35110
Chromobacterium violaceum ATCC 12472
Chromohalobacter salexigens DSM 3043
Citrobacter koseri ATCC BAA 895
Citrobacter rodentium ICC168
Clavibacter michiganensis subsp michiganensis NCPPB 382
Clostridium acetobutylicum ATCC 824
Clostridium beijerinckii NCIMB 8052
Clostridium botulinum A str ATCC 3502
Clostridium cellulolyticum H10
Clostridium cellulovorans 743B
Clostridium difficile 630
Clostridium kluyveri DSM 555
Clostridium lentocellum DSM 5427
Clostridium ljungdahlii DSM 13528
Clostridium novyi NT
Clostridium perfringens ATCC 13124
Clostridium phytofermentans ISDg
Clostridium saccharolyticum WM1
Clostridium sp SY8519
Clostridium sticklandii DSM 519
Clostridium tetani E88
Clostridium thermocellum ATCC 27405
Collimonas fungivorans Ter331
Colwellia psychrerythraea 34H
Comamonas testosteroni CNB 2
Conexibacter woesei DSM 14684
Coprothermobacter proteolyticus DSM 5265
Coraliomargarita akajimensis DSM 45221
Coriobacterium glomerans PW2
Corynebacterium aurimucosum ATCC 700975
Corynebacterium diphtheriae NCTC 13129
Corynebacterium efficiens YS 314
Corynebacterium glutamicum ATCC 13032
Corynebacterium jeikeium K411
Corynebacterium kroppenstedtii DSM 44385
Corynebacterium pseudotuberculosis FRC41
Corynebacterium resistens DSM 45100
Corynebacterium ulcerans 809
Corynebacterium urealyticum DSM 7109
Corynebacterium variabile DSM 44702
Coxiella burnetii RSA 493
Croceibacter atlanticus HTCC2559
Cronobacter sakazakii ATCC BAA 894
Cronobacter turicensis z3032
Cryptobacterium curtum DSM 15641
Cupriavidus metallidurans CH34
Cupriavidus necator N 1
Cupriavidus taiwanensis LMG 19424
cyanobacterium UCYN A
Cyanothece sp ATCC 51142
Cyclobacterium marinum DSM 745
Cytophaga hutchinsonii ATCC 33406
Dechloromonas aromatica RCB
Deferribacter desulfuricans SSM1
Dehalococcoides ethenogenes 195
Dehalococcoides sp BAV1
Dehalogenimonas lykanthroporepellens BL DC 9
Deinococcus deserti VCD115 Deinococcus geothermalis DSM 11300
Deinococcus maricopensis DSM 21211
Deinococcus proteolyticus MRP
Deinococcus radiodurans R1
Delftia acidovorans SPH 1 Delftia sp Cs1 4
Denitrovibrio acetiphilus DSM 12809
Desulfarculus baarsii DSM 2075
Desulfatibacillum alkenivorans AK 01
Desulfitobacterium hafniense Y51
Desulfobacca acetoxidans DSM 11109
Desulfobacterium autotrophicum HRM2
Desulfobulbus propionicus DSM 2032
Desulfococcus oleovorans Hxd3
Desulfohalobium retbaense DSM 5692
Desulfomicrobium baculatum DSM 4028
Desulfotalea psychrophila LSv54
Desulfotomaculum acetoxidans DSM 771
Desulfotomaculum carboxydivorans CO 1 SRB
Desulfotomaculum kuznetsovii DSM 6115
Desulfotomaculum reducens MI 1
Desulfotomaculum ruminis DSM 2154
Desulfovibrio aespoeensis Aspo 2
Desulfovibrio africanus str Walvis Bay
Desulfovibrio alaskensis G20
Desulfovibrio desulfuricans ND132
Desulfovibrio magneticus RS 1
Desulfovibrio salexigens DSM 2638
Desulfovibrio vulgaris RCH1
Desulfurispirillum indicum S5
Desulfurivibrio alkaliphilus AHT2
Desulfurobacterium thermolithotrophum DSM 11699
Desulfurococcus kamchatkensis 1221n
Desulfurococcus mucosus DSM 2162
Dichelobacter nodosus VCS1703A
Dickeya dadantii 3937
Dickeya zeae Ech1591
Dictyoglomus thermophilum H 6 12
Dictyoglomus turgidum DSM 6724
Dinoroseobacter shibae DFL 12
Dyadobacter fermentans DSM 18053
Edwardsiella ictaluri 93 146
Edwardsiella tarda EIB202
Eggerthella lenta DSM 2243
Eggerthella sp YY7918
Ehrlichia canis str Jake
Ehrlichia chaffeensis str Arkansas
Ehrlichia ruminantium str Welgevonden
Elusimicrobium minutum Pei191
Enterobacter aerogenes KCTC 2190
Enterobacter asburiae LF7a
Enterobacter cloacae subsp cloacae ATCC 13047
Enterobacter sp 638 Enterococcus faecalis V583
Erwinia amylovora ATCC 49946
Erwinia billingiae Eb661
Erwinia pyrifoliae DSM 12163
Erwinia sp Ejp617
Erwinia tasmaniensis Et1 99
Erysipelothrix rhusiopathiae
Erythrobacter litoralis HTCC2594
Escherichia coli O157:H7 str Sakai
Escherichia fergusonii ATCC 35469
Ethanoligenens harbinense YUAN 3
Eubacterium eligens ATCC 27750
Eubacterium limosum KIST612
Eubacterium rectale ATCC 33656
Exiguobacterium sibiricum 25515
Exiguobacterium sp AT1b
Ferrimonas balearica DSM 9799
Ferroglobus placidus DSM 10642
Fervidobacterium nodosum Rt17 B1
Fibrobacter succinogenes subsp succinogenes S85
Filifactor alocis ATCC 35896
Finegoldia magna ATCC 29328
Flavobacteriaceae bacterium 3519 10
Flavobacterium branchiophilum FL 15
Flavobacterium columnare ATCC 49512
Flavobacterium johnsoniae UW101
Flavobacterium psychrophilum JIP02 86
Flexistipes sinusarabici DSM 4947
Fluviicola taffensis DSM 16823
Francisella novicida U112
Francisella philomiragia subsp philomiragia ATCC 25017
Francisella sp TX077308
Francisella tularensis subsp holarctica LVS
Frankia alni ACN14a
Frankia sp CcI3
Frankia symbiont of Datisca glomerata
Fusobacterium nucleatum subsp nucleatum ATCC 25586
Gallibacterium anatis UMN179
Gallionella capsiferriformans ES 2 gamma proteobacterium HdN1
Gardnerella vaginalis 409 05
Gemmatimonas aurantiaca T 27
Geobacillus kaustophilus HTA426
Geobacillus sp C56 T3
Geobacillus thermodenitrificans NG80 2
Geobacillus thermoglucosidasius C56 YS93
Geobacillus thermoleovorans CCB US3 UF5
Geobacter bemidjiensis Bem
Geobacter daltonii FRC 32
Geobacter lovleyi SZ
Geobacter metallireducens GS 15
Geobacter sp M18
Geobacter sulfurreducens PCA
Geobacter uraniireducens Rf4
Geodermatophilus obscurus DSM 43160
Glaciecola nitratireducens FR1064
Glaciecola sp 4H 3 7YE 5
Gloeobacter violaceus PCC 7421
Gluconacetobacter diazotrophicus PAl 5
Gluconacetobacter xylinus NBRC 3288
Gluconobacter oxydans 621H
Gordonia bronchialis DSM 43247
Gramella forsetii KT0803
Granulibacter bethesdensis CGDNIH1
Granulicella mallensis MP5ACTX8
Granulicella tundricola
Haemophilus ducreyi 35000HP
Haemophilus influenzae 10810
Haemophilus parainfluenzae T3T1
Haemophilus parasuis SH0165
Haemophilus somnus 129PT
Hahella chejuensis KCTC 2396
Halalkalicoccus jeotgali B3
Halanaerobium hydrogeniformans
Haliangium ochraceum DSM 14365
Haliscomenobacter hydrossis DSM 1100
Haloarcula hispanica ATCC 33960
Haloarcula marismortui ATCC 43049
Halobacterium sp NRC 1
Haloferax volcanii DS2
Halogeometricum borinquense DSM 11551
Halomicrobium mukohataei DSM 12286
Halomonas elongata DSM 2581
halophilic archaeon DL31
Halopiger xanaduensis SH 6
Haloquadratum walsbyi C23
Halorhabdus utahensis DSM 12940
Halorhodospira halophila SL1
Halorubrum lacusprofundi ATCC 49239
Haloterrigena turkmenica DSM 5511
Halothermothrix orenii H 168
Halothiobacillus neapolitanus c2
Helicobacter acinonychis str Sheeba
Helicobacter bizzozeronii CIII 1
Helicobacter felis ATCC 49179
Helicobacter hepaticus ATCC 51449
Helicobacter mustelae 12198
Helicobacter pylori 26695
Heliobacterium modesticaldum Ice1
Herbaspirillum seropedicae SmR1
Herminiimonas arsenicoxydans
Herpetosiphon aurantiacus DSM 785
Hippea maritima DSM 10411
Hirschia baltica ATCC 49814
Hydrogenobacter thermophilus TK 6
Hydrogenobaculum sp Y04AAS1
Hyperthermus butylicus DSM 5456
Hyphomicrobium denitrificans ATCC 51888
Hyphomicrobium sp
Hyphomonas neptunium ATCC 15444
Idiomarina loihiensis L2TR
Ignicoccus hospitalis KIN4 I
Ignisphaera aggregans DSM 17230
Ilyobacter polytropus DSM 2926
Intrasporangium calvum DSM 43043
Isoptericola variabilis 225
Isosphaera pallida ATCC 43644
Jannaschia sp CCS1
Janthinobacterium sp Marseille
Jonesia denitrificans DSM 20603
Kangiella koreensis DSM 16069
Ketogulonicigenium vulgare WSH 001
Kineococcus radiotolerans SRS30216
Kitasatospora setae KM 6054
Klebsiella oxytoca KCTC 1686
Klebsiella pneumoniae 342
Klebsiella variicola At 22
Kocuria rhizophila DC2201
Kosmotoga olearia TBF 1951
Kribbella flavida DSM 17836
Krokinobacter sp 4H 3 7 5
Kyrpidia tusciae DSM 2912
Kytococcus sedentarius DSM 20547
Lacinutrix sp 5H 3 7 4
Lactobacillus acidophilus NCFM
Lactobacillus amylovorus GRL 1112
Lactobacillus brevis ATCC 367
Lactobacillus buchneri NRRL B 30929
Lactobacillus casei ATCC 334
Lactobacillus crispatus ST1
Lactobacillus delbrueckii subsp bulgaricus ATCC 11842
Lactobacillus fermentum IFO 3956
Lactobacillus gasseri ATCC 33323
Lactobacillus helveticus DPC 4571
Lactobacillus johnsonii NCC 533
Lactobacillus kefiranofaciens ZW3
Lactobacillus plantarum subsp plantarum ST III
Lactobacillus reuteri DSM 20016
Lactobacillus rhamnosus ATCC 8530
Lactobacillus ruminis ATCC 27782
Lactobacillus sakei subsp sakei 23K
Lactobacillus salivarius UCC118
Lactobacillus sanfranciscensis TMW 11304
Lactococcus garvieae ATCC 49156
Lactococcus lactis subsp cremoris NZ9000
Laribacter hongkongensis HLHK9
Lawsonia intracellularis PHE MN1 00
Leadbetterella byssophila DSM 17132
Legionella longbeachae NSW150
Legionella pneumophila subsp pneumophila ATCC 43290
Leifsonia xyli subsp xyli str CTCB07
Leptospira biflexa serovar Patoc strain Patoc 1 Ames
Leptospira borgpetersenii serovar Hardjo bovis str L550
Leptospira interrogans serovar Copenhageni str Fiocruz L1 130
Leptothrix cholodnii SP 6
Leptotrichia buccalis C 1013 b
Leuconostoc citreum KM20
Leuconostoc gasicomitatum LMG 18811
Leuconostoc kimchii IMSNU 11154
Leuconostoc mesenteroides subsp mesenteroides ATCC 8293
Leuconostoc sp C2 Listeria innocua Clip11262 Listeria ivanovii
Listeria monocytogenes EGD e
Listeria seeligeri serovar 1 2b str SLCC3954
Listeria welshimeri serovar 6b str SLCC5334
Lysinibacillus sphaericus C3 41
Macrococcus caseolyticus JCSC5402
Magnetococcus marinus MC 1
Magnetospirillum magneticum AMB 1
Mahella australiensis 50 1 BON
Mannheimia succiniciproducens MBEL55E
Maribacter sp HTCC2170
Maricaulis maris MCS10
Marinithermus hydrothermalis DSM 14884
Marinobacter adhaerens HP15
Marinobacter aquaeolei VT8
Marinomonas mediterranea MMB 1
Marinomonas posidonica IVIA Po 181
Marinomonas sp MWYL1
Marivirga tractuosa DSM 4126
Megasphaera elsdenii
Meiothermus ruber DSM 1279
Meiothermus silvanus DSM 9946
Melissococcus plutonius ATCC 35311
Mesoplasma florum L1
Mesorhizobium ciceri biovar biserrulae WSM1271
Mesorhizobium loti MAFF303099
Mesorhizobium opportunistum WSM2075
Metallosphaera cuprina Ar 4
Metallosphaera sedula DSM 5348
Methanobacterium sp AL 21
Methanobrevibacter ruminantium M1
Methanobrevibacter smithii ATCC 35061
Methanocaldococcus fervens AG86
Methanocaldococcus infernus ME
Methanocaldococcus jannaschii DSM 2661
Methanocaldococcus sp FS406 22
Methanocaldococcus vulcanius M7
Methanocella arvoryzae MRE50
Methanocella paludicola SANAE
Methanococcoides burtonii DSM 6242
Methanococcus aeolicus Nankai 3
Methanococcus maripaludis S2
Methanococcus vannielii SB
Methanococcus voltae A3
Methanocorpusculum labreanum Z
Methanoculleus marisnigri JR1
Methanohalobium evestigatum Z 7303
Methanohalophilus mahii DSM 5219
Methanoplanus petrolearius DSM 11571
Methanopyrus kandleri AV19
Methanoregula boonei 6A8
Methanosaeta concilii GP6
Methanosaeta thermophila PT
Methanosalsum zhilinae DSM 4017
Methanosarcina acetivorans C2A
Methanosarcina barkeri str Fusaro
Methanosarcina mazei Go1
Methanosphaera stadtmanae DSM 3091
Methanosphaerula palustris E1 9c
Methanospirillum hungatei JF 1
Methanothermobacter marburgensis str Marburg
Methanothermobacter thermautotrophicus str Delta H
Methanothermococcus okinawensis IH1
Methanothermus fervidus DSM 2088
Methanotorris igneus Kol 5
Methylacidiphilum infernorum V4
Methylibium petroleiphilum PM1
Methylobacillus flagellatus KT
Methylobacterium chloromethanicum CM4
Methylobacterium extorquens AM1
Methylobacterium nodulans ORS 2060
Methylobacterium populi BJ001
Methylobacterium radiotolerans JCM 2831
Methylobacterium sp 4 46
Methylocella silvestris BL2
Methylococcus capsulatus str Bath
Methylomicrobium alcaliphilum
Methylomonas methanica MC09
Methylotenera mobilis JLW8
Methylotenera versatilis 301
Methylovorus glucosetrophus SIP3 4
Methylovorus sp MP688
Micavibrio aeruginosavorus ARL 13
Microbacterium testaceum StLB037
Micrococcus luteus NCTC 2665
Microcystis aeruginosa NIES 843
Microlunatus phosphovorus NM 1
Micromonospora aurantiaca ATCC 27029
Micromonospora sp L5
Mobiluncus curtisii ATCC 43063
Moorella thermoacetica ATCC 39073
Moraxella catarrhalis RH4
Muricauda ruestringensis DSM 13258
Mycobacterium abscessus ATCC 19977
Mycobacterium africanum GM041182
Mycobacterium avium 104
Mycobacterium bovis AF2122 97
Mycobacterium canettii CIPT 140010059
Mycobacterium gilvum PYR GCK
Mycobacterium leprae TN
Mycobacterium marinum M
Mycobacterium rhodesiae NBB3
Mycobacterium smegmatis str MC2 155
Mycobacterium sp JDM601
Mycobacterium tuberculosis H37Rv
Mycobacterium ulcerans Agy99
Mycobacterium vanbaalenii PYR 1
Mycoplasma agalactiae PG2
Mycoplasma arthritidis 158L3 1
Mycoplasma bovis PG45
Mycoplasma capricolum subsp capricolum ATCC 27343
Mycoplasma conjunctivae HRC 581
Mycoplasma crocodyli MP145
Mycoplasma gallisepticum str Rlow
Mycoplasma genitalium G37
Mycoplasma haemocanis str Illinois
Mycoplasma haemofelis str Langford 1
Mycoplasma hominis
Mycoplasma hyopneumoniae 232
Mycoplasma hyorhinis HUB 1
Mycoplasma leachii 99 014 6
Mycoplasma mobile 163K
Mycoplasma mycoides subsp mycoides SC str PG1
Mycoplasma penetrans HF 2
Mycoplasma pneumoniae M129
Mycoplasma pulmonis UAB CTIP
Mycoplasma putrefaciens KS1
Mycoplasma suis str Illinois
Mycoplasma synoviae 53
Myxococcus fulvus HW 1
Myxococcus xanthus DK 1622
Nakamurella multipartita DSM 44233
Nanoarchaeum equitans Kin4 M
Natranaerobius thermophilus JW NM WN LF
Natrialba magadii ATCC 43099
Natronomonas pharaonis DSM 2160
Nautilia profundicola AmH Neisseria gonorrhoeae FA 1090
Neisseria lactamica 020 06
Neisseria meningitidis M01 240149
Neorickettsia risticii str Illinois
Neorickettsia sennetsu str Miyayama
Niastella koreensis GR20 10
Nitratifractor salsuginis DSM 16511
Nitratiruptor sp SB155 2
Nitrobacter hamburgensis X14
Nitrobacter winogradskyi Nb 255
Nitrosococcus halophilus Nc4
Nitrosococcus oceani ATCC 19707
Nitrosococcus watsonii C 113
Nitrosomonas europaea ATCC 19718
Nitrosomonas eutropha C91
Nitrosomonas sp AL212
Nitrosopumilus maritimus SCM1
Nitrosospira multiformis ATCC 25196
Nocardia farcinica IFM 10152
Nocardioides sp JS614
Nocardiopsis dassonvillei subsp dassonvillei DSM 43111
Nostoc azollae 0708
Nostoc punctiforme PCC 73102
Nostoc sp PCC 7120
Novosphingobium aromaticivorans DSM 12444
Novosphingobium sp PP1Y Oceanithermus profundus DSM 14977
Oceanobacillus iheyensis HTE831
Ochrobactrum anthropi ATCC 49188
Odoribacter splanchnicus DSM 20712
Oenococcus oeni PSU 1
Oligotropha carboxidovorans OM5
Olsenella uli DSM 7084
Onion yellows phytoplasma OY M
Opitutus terrae PB90 1
Orientia tsutsugamushi str Boryong
Oscillibacter valericigenes
Owenweeksia hongkongensis DSM 17368
Paenibacillus mucilaginosus KNP414
Paenibacillus polymyxa E681
Paenibacillus sp JDR 2
Paenibacillus terrae HPL 003
Paludibacter propionicigenes WB4
Pantoea ananatis LMG 20103
Pantoea sp At 9b
Pantoea vagans C9 1
Parabacteroides distasonis ATCC 8503
Parachlamydia acanthamoebae UV 7
Paracoccus denitrificans PD1222
Parvibaculum lavamentivorans DS 1
Parvularcula bermudensis HTCC2503
Pasteurella multocida subsp multocida str Pm70
Pectobacterium atrosepticum SCRI1043
Pectobacterium carotovorum subsp carotovorum PC1
Pectobacterium wasabiae WPP163
Pediococcus pentosaceus ATCC 25745
Pedobacter heparinus DSM 2366
Pedobacter saltans DSM 12145
Pelagibacterium halotolerans B2
Pelobacter carbinolicus DSM 2380
Pelobacter propionicus DSM 2379
Pelodictyon phaeoclathratiforme BU 1
Pelotomaculum thermopropionicum SI
Persephonella marina EX H1
Petrotoga mobilis SJ95
Phenylobacterium zucineum HLK1
Photobacterium profundum SS9
Photorhabdus asymbiotica subsp asymbiotica ATCC 43949
Photorhabdus luminescens subsp laumondii TTO1
Picrophilus torridus DSM 9790
Pirellula staleyi DSM 6068
Planctomyces brasiliensis DSM 5305
Planctomyces limnophilus DSM 3776
Polaromonas naphthalenivorans CJ2
Polaromonas sp JS666
Polymorphum gilvum SL003B 26A1
Polynucleobacter necessarius subsp asymbioticus QLW P1DMWA 1
Porphyromonas asaccharolytica DSM 20707
Porphyromonas gingivalis W83
Prevotella denticola F0289
Prevotella melaninogenica ATCC 25845
Prevotella ruminicola 23
Prochlorococcus marinus str MIT 9215
Propionibacterium acnes 6609
Propionibacterium freudenreichii subsp shermanii CIRM BIA1
Prosthecochloris aestuarii DSM 271
Proteus mirabilis HI4320
Pseudoalteromonas atlantica T6c
Pseudoalteromonas haloplanktis TAC125
Pseudoalteromonas sp SM9913
Pseudogulbenkiania sp NH8B
Pseudomonas aeruginosa PAO1
Pseudomonas brassicacearum subsp brassicacearum NFM421
Pseudomonas entomophila L48
Pseudomonas fluorescens F113
Pseudomonas fulva 12 X
Pseudomonas mendocina ymp
Pseudomonas protegens Pf 5
Pseudomonas putida F1
Pseudomonas stutzeri A1501
Pseudomonas syringae pv phaseolicola 1448A
Pseudonocardia dioxanivorans CB1190
Pseudovibrio sp FO BEG1
Pseudoxanthomonas spadix BD a59
Pseudoxanthomonas suwonensis 11 1
Psychrobacter arcticus 273 4
Psychrobacter cryohalolentis K5
Psychrobacter sp PRwf 1
Psychromonas ingrahamii 37
Pusillimonas sp T7 7
Pyrobaculum aerophilum str IM2
Pyrobaculum arsenaticum DSM 13514
Pyrobaculum calidifontis JCM 11548
Pyrobaculum islandicum DSM 4184
Pyrobaculum neutrophilum V24Sta
Pyrobaculum sp 1860
Pyrococcus abyssi GE5
Pyrococcus furiosus DSM 3638
Pyrococcus horikoshii OT3
Pyrococcus sp NA2
Pyrococcus yayanosii CH1
Pyrolobus fumarii 1A
Rahnella sp Y9602
Ralstonia eutropha JMP134
Ralstonia pickettii 12D
Ralstonia solanacearum GMI1000
Ramlibacter tataouinensis TTB310
Renibacterium salmoninarum ATCC 33209
Rhizobium etli CFN 42
Rhizobium leguminosarum bv viciae 3841
Rhodobacter capsulatus SB 1003
Rhodobacter sphaeroides 241
Rhodococcus equi 103S
Rhodococcus erythropolis PR4
Rhodococcus jostii RHA1
Rhodococcus opacus B4
Rhodoferax ferrireducens T118
Rhodomicrobium vannielii ATCC 17100
Rhodopirellula baltica SH 1
Rhodopseudomonas palustris CGA009
Rhodospirillum centenum SW
Rhodospirillum rubrum ATCC 11170
Rhodothermus marinus DSM 4252
Rickettsia africae ESF 5
Rickettsia akari str Hartford
Rickettsia bellii RML369 C
Rickettsia canadensis str McKiel
Rickettsia conorii str Malish 7
Rickettsia felis URRWXCal2
Rickettsia heilongjiangensis 054
Rickettsia japonica YH
Rickettsia massiliae MTU5
Rickettsia peacockii str Rustic
Rickettsia prowazekii str Madrid E
Rickettsia rickettsii str Iowa
Rickettsia sibirica 246
Rickettsia slovaca 13 B
Rickettsia typhi str Wilmington
Riemerella anatipestifer ATCC 11845 DSM 15868
Robiginitalea biformata HTCC2501
Roseburia hominis A2 183
Roseiflexus castenholzii DSM 13941
Roseiflexus sp RS 1
Roseobacter denitrificans OCh 114
Roseobacter litoralis Och 149
Rothia dentocariosa ATCC 17931
Rothia mucilaginosa DY 18
Rubrobacter xylanophilus DSM 9941
Ruegeria pomeroyi DSS 3
Ruegeria sp TM1040
Ruminococcus albus 7
Runella slithyformis DSM 19594
Saccharomonospora viridis DSM 43017
Saccharophagus degradans 2 40
Saccharopolyspora erythraea NRRL 2338
Salinibacter ruber DSM 13855
Salinispora arenicola CNS 205
Salinispora tropica CNB 440
Salmonella bongori NCTC 12419
Salmonella enterica subsp enterica serovar Enteritidis str P125109
Sanguibacter keddieii DSM 10542
Sebaldella termitidis ATCC 33386
Segniliparus rotundus DSM 44985
Selenomonas sputigena ATCC 35185
Serratia plymuthica AS9
Serratia proteamaculans 568 Serratia sp AS12
Serratia symbiotica str Cinara cedri
Shewanella amazonensis SB2B
Shewanella baltica OS155
Shewanella denitrificans OS217
Shewanella frigidimarina NCIMB 400
Shewanella halifaxensis HAW EB4
Shewanella loihica PV 4
Shewanella oneidensis MR 1
Shewanella pealeana ATCC 700345
Shewanella piezotolerans WP3
Shewanella putrefaciens CN 32
Shewanella sediminis HAW EB3
Shewanella sp ANA 3
Shewanella violacea DSS12
Shewanella woodyi ATCC 51908
Shigella boydii Sb227
Shigella dysenteriae Sd197
Shigella flexneri 2a str 301
Shigella sonnei Ss046
Sideroxydans lithotrophicus ES 1
Simkania negevensis Z
Sinorhizobium fredii NGR234
Sinorhizobium medicae WSM419
Sinorhizobium meliloti 1021
Slackia heliotrinireducens DSM 20476
Sodalis glossinidius str morsitans
Sorangium cellulosum So ce56
Sphaerobacter thermophilus DSM 20745
Sphaerochaeta coccoides DSM 17374
Sphaerochaeta globus str Buddy
Sphaerochaeta pleomorpha str Grapes
Sphingobacterium sp 21
Sphingobium chlorophenolicum L 1
Sphingobium japonicum UT26S
Sphingobium sp SYK 6
Sphingomonas wittichii RW1
Sphingopyxis alaskensis RB2256
Spirochaeta caldaria DSM 7334
Spirochaeta smaragdinae DSM 11293
Spirochaeta thermophila DSM 6192
Spirosoma linguale DSM 74
Stackebrandtia nassauensis DSM 44728
Staphylococcus aureus subsp aureus JH1
Staphylococcus carnosus subsp carnosus TM300
Staphylococcus epidermidis ATCC 12228
Staphylococcus haemolyticus JCSC1435
Staphylococcus lugdunensis HKU09 01
Staphylococcus pseudintermedius HKU10 03
Staphylothermus hellenicus DSM 12710
Staphylothermus marinus F1
Starkeya novella DSM 506
Stenotrophomonas maltophilia K279a
Stigmatella aurantiaca DW4 3 1
Streptobacillus moniliformis DSM 12112
Streptococcus agalactiae 2603V R
Streptococcus dysgalactiae subsp equisimilis ATCC 12394
Streptococcus equi subspecies zooepidemicus
Streptococcus gallolyticus subsp gallolyticus ATCC BAA 2069
Streptococcus gordonii str Challis substr CH1
Streptococcus macedonicus ACA DC 198
Streptococcus mitis B6
Streptococcus mutans NN2025
Streptococcus oralis Uo5
Streptococcus parasanguinis ATCC 15912
Streptococcus parauberis KCTC 11537
Streptococcus pasteurianus ATCC 43144
Streptococcus pneumoniae ST556
Streptococcus pseudopneumoniae IS7493
Streptococcus pyogenes M1 GAS
Streptococcus salivarius JIM8780
Streptococcus sanguinis SK36
Streptococcus suis 05ZYH33
Streptococcus thermophilus CNRZ1066
Streptococcus uberis 0140J
Streptomyces avermitilis MA 4680
Streptomyces bingchenggensis BCW 1
Streptomyces cattleya NRRL 8057 DSM 46488
Streptomyces coelicolor A32
Streptomyces flavogriseus ATCC 33331
Streptomyces griseus subsp griseus NBRC 13350
Streptomyces scabiei 8722
Streptomyces sp SirexAA E
Streptomyces violaceusniger Tu 4113
Streptosporangium roseum DSM 43021
Sulfobacillus acidophilus DSM 10332
Sulfolobus acidocaldarius DSM 639
Sulfolobus islandicus M1425
Sulfolobus solfataricus P2
Sulfolobus tokodaii str 7
Sulfuricurvum kujiense DSM 16994
Sulfurihydrogenibium azorense Az Fu1
Sulfurihydrogenibium sp YO3AOP1
Sulfurimonas autotrophica DSM 16294
Sulfurimonas denitrificans DSM 1251
Sulfurospirillum deleyianum DSM 6946
Sulfurovum sp NBC37 1
Symbiobacterium thermophilum IAM 14863
Synechococcus elongatus PCC 6301
Synechococcus sp CC9605
Synechocystis sp PCC 6803
Syntrophobacter fumaroxidans MPOB
Syntrophobotulus glycolicus DSM 8271
Syntrophomonas wolfei subsp wolfei str Goettingen
Syntrophothermus lipocalidus DSM 12680
Syntrophus aciditrophicus SB
Tannerella forsythia ATCC 43037
Taylorella equigenitalis MCE9
Tepidanaerobacter acetatoxydans Re1
Teredinibacter turnerae T7901
Terriglobus saanensis SP1PR4
Tetragenococcus halophilus
Thauera sp MZ1T
Thermaerobacter marianensis DSM 12885
Thermanaerovibrio acidaminovorans DSM 6589
Thermincola potens JR
Thermoanaerobacter brockii subsp finnii Ako 1
Thermoanaerobacter italicus Ab9
Thermoanaerobacterium thermosaccharolyticum DSM 571
Thermoanaerobacterium xylanolyticum LX 11
Thermoanaerobacter mathranii subsp mathranii str A3
Thermoanaerobacter pseudethanolicus ATCC 33223
Thermoanaerobacter sp X513
Thermoanaerobacter tengcongensis MB4
Thermoanaerobacter wiegelii Rt8B1
Thermobaculum terrenum ATCC BAA 798
Thermobifida fusca YX
Thermobispora bispora DSM 43833
Thermococcus barophilus MP
Thermococcus gammatolerans EJ3
Thermococcus kodakarensis KOD1
Thermococcus onnurineus NA1
Thermococcus sibiricus MM 739
Thermococcus sp 4557
Thermocrinis albus DSM 14484
Thermodesulfatator indicus DSM 15286
Thermodesulfobacterium sp OPB45
Thermodesulfobium narugense DSM 14796
Thermodesulfovibrio yellowstonii DSM 11347
Thermofilum pendens Hrk 5
Thermomicrobium roseum DSM 5159
Thermomonospora curvata DSM 43183
Thermoplasma acidophilum DSM 1728
Thermoplasma volcanium GSS1
Thermoproteus uzoniensis 76820
Thermosediminibacter oceani DSM 16646
Thermosipho africanus TCF52B
Thermosipho melanesiensis BI429
Thermosphaera aggregans DSM 11486
Thermosynechococcus elongatus BP 1
Thermotoga lettingae TMO
Thermotoga maritima MSB8
Thermotoga naphthophila RKU 10
Thermotoga neapolitana DSM 4359
Thermotoga petrophila RKU 1
Thermotoga sp RQ2
Thermotoga thermarum DSM 5069
Thermovibrio ammonificans HB 1
Thermovirga lienii DSM 17291
Thermus scotoductus SA 01
Thermus sp CCB US3 UF1
Thermus thermophilus HB27
Thioalkalimicrobium cyclicum ALM1
Thioalkalivibrio sp K90mix
Thioalkalivibrio sulfidophilus HL EbGr7
Thiobacillus denitrificans ATCC 25259
Thiomicrospira crunogena XCL 2
Thiomonas intermedia K12
Tolumonas auensis DSM 9187
Treponema azotonutricium ZAS 9
Treponema brennaborense DSM 12168
Treponema denticola ATCC 35405
Treponema pallidum subsp pallidum str Nichols
Treponema paraluiscuniculi Cuniculi A
Treponema primitia ZAS 2
Treponema succinifaciens DSM 2489
Trichodesmium erythraeum IMS101
Tropheryma whipplei str Twist
Truepera radiovictrix DSM 17093
Tsukamurella paurometabola DSM 20162
Ureaplasma parvum serovar 3 str ATCC 27815
Ureaplasma urealyticum serovar 10 str ATCC 33699
Variovorax paradoxus S110
Veillonella parvula DSM 2008
Verminephrobacter eiseniae EF01 2
Verrucosispora maris AB 18 032
Vibrio anguillarum 775
Vibrio cholerae O1 biovar El Tor str N16961
Vibrio fischeri ES114
Vibrio furnissii NCTC 11218
Vibrio harveyi ATCC BAA 1116
Vibrio parahaemolyticus RIMD 2210633
Vibrio sp EJY3
Vibrio splendidus LGP32
Vibrio vulnificus CMCP6
Vulcanisaeta distributa DSM 14429
Vulcanisaeta moutnovskia 768 28
Waddlia chondrophila WSU 86 1044
Weeksella virosa DSM 16922
Weissella koreensis KACC 15510
Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis
Wolbachia endosymbiont of Culex quinquefasciatus Pel Wolbachia sp wRi
Wolinella succinogenes DSM 1740
Xanthobacter autotrophicus Py2
Xanthomonas albilineans GPE PC73
Xanthomonas axonopodis pv citri str 306
Xanthomonas campestris pv campestris str 8004
Xanthomonas oryzae pv oryzae KACC 10331
Xenorhabdus bovienii SS 2004
Xenorhabdus nematophila ATCC 19061
Xylanimonas cellulosilytica DSM 15894
Xylella fastidiosa 9a5c
Yersinia enterocolitica subsp enterocolitica 8081
Yersinia pestis CO92
Yersinia pseudotuberculosis IP 32953
Zobellia galactanivorans
Zunongwangia profunda SM A87
Zymomonas mobilis subsp mobilis ATCC 10988