Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2.
Bioinformatics
; 28(7): 1033-4, 2012 Apr 01.
Article
em En
| MEDLINE
| ID: mdl-22332237
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.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Filogenia
/
Bactérias
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Archaea
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Biologia Computacional
/
Genômica
Idioma:
En
Ano de publicação:
2012
Tipo de documento:
Article