PT  - JOURNAL ARTICLE
AU  - Leo Kaindl
AU  - Corinn Small
AU  - Remco Stam
TI  - AB12PHYLO: an integrated pipeline for Maximum Likelihood phylogenetic inference from ABI trace data
AID  - 10.1101/2021.03.01.433007
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.03.01.433007
4099  - http://biorxiv.org/content/early/2021/08/19/2021.03.01.433007.short
4100  - http://biorxiv.org/content/early/2021/08/19/2021.03.01.433007.full
AB  - Multi-gene phylogenies constructed from multiplexed and Sanger sequencing data are regularly used in mycology and other disciplines as a cost-effective way of species identification and as a first means to investigate genetic diversity samples.Today, a number of tools exist for each of the steps in this analysis, including quality control and trimming, the generation of a multiple sequence alignment (MSA), extraction of informative sites, and the construction of the final phylogenetic tree. A BLAST search in a reference database is often performed to identify sequences of type specimens to compare the samples with in the phylogeny. Made over the past decades, these tools are all independent from and often not perfectly adapted to one another.We present AB12PHYLO, an integrated pipeline that can perform all necessary steps from reading in raw Sanger sequencing data through visualizing and editing phylogenies. In addition, AB12PHYLO can calculate basic summary statistics for each gene in the phylogeny.AB12PHYLO is designed as a wrapper of several open access and commonly used tools for each of the intermediate stages, and intended to simplify the phylogenetic pipeline while still allowing a high degree of access. It comes as a command-line version for the highest reproducibility and an intuitive graphical user interface (GUI) for easy adoption by IT-agnostic end-users. The use of AB12PHYLO significantly reduces the hands-on working time for these analyses.Competing Interest StatementThe authors have declared no competing interest.