We describe MUSCLE, a new computer program for creating multiple alignments of protein
sequences. Elements of the algorithm include fast distance estimation using k mer counting, …

Background In a previous paper, we introduced MUSCLE, a new program for creating multiple
alignments of protein sequences, giving a brief summary of the algorithm and showing …

Amplicon sequencing of tags such as 16S and ITS ribosomal RNA is a popular method for
investigating microbial populations. In such experiments, sequence errors caused by PCR …

Multiple sequence alignments are an essential tool for protein structure and function prediction,
phylogeny inference and other common tasks in sequence analysis. Recently developed …

Motivation: Chimeric DNA sequences often form during polymerase chain reaction
amplification, especially when sequencing single regions (eg 16S rRNA or fungal Internal …

Motivation: Biological sequence data is accumulating rapidly, motivating the development of
improved high-throughput methods for sequence classification. Results: UBLAST and …

Amplified marker-gene sequences can be used to understand microbial community structure,
but they suffer from a high level of sequencing and amplification artifacts. The UPARSE …

Land plants associate with a root microbiota distinct from the complex microbial community
present in surrounding soil. The microbiota colonizing the rhizosphere (immediately …

To understand the biology and evolution of ruminants, the cattle genome was sequenced to
about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a …

Motivation: Next-generation sequencing produces vast amounts of data with errors that are
difficult to distinguish from true biological variation when coverage is low. Results: We …