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Bioinformatics. 2012 Apr 1;28(7):1033-4. doi: 10.1093/bioinformatics/bts079. Epub 2012 Feb 12.

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2.

Author information

1
Department of Biology, University of Virginia, Charlottesville, VA 22904, USA. mw4yv@virginia.edu

Abstract

SUMMARY:

With the explosive growth of bacterial and archaeal sequence data, large-scale phylogenetic analyses present both opportunities and challenges. Here we describe AMPHORA2, an automated phylogenomic inference tool that can be used for high-throughput, high-quality genome tree reconstruction and metagenomic phylotyping. Compared with its predecessor, AMPHORA2 has several major enhancements and new functions: it has a greatly expanded phylogenetic marker database and can analyze both bacterial and archaeal sequences; it incorporates probability-based sequence alignment masks that improve the phylogenetic accuracy; it can analyze DNA as well as protein sequences and is more sensitive in marker identification; finally, it is over 100× faster in metagenomic phylotyping.

AVAILABILITY:

http://wolbachia.biology.virginia.edu/WuLab/Software.html.

CONTACT:

mw4yv@virginia.edu

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
22332237
DOI:
10.1093/bioinformatics/bts079
[Indexed for MEDLINE]

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