Tag: Phylogenomic Inference

Phyla_AMPHORA – Phylum-specific Automated Phylogenomic Inference Pipeline for Bacterial Sequences

Phyla_AMPHORA

:: DESCRIPTION

Phyla_AMPHORA is a flavor of AMPHOR2 that performs large-scale phylogenetic inference using phylum-specific bacterial phylogenetic markers. The current version contains a total of 7542 marker genes from 20 bacterial phyla. With the vastly expanded phylogenetic marker database, Phyla_AMPHORA increases the robustness of the genome trees as well as the power of metagenomic phylotyping.

::DEVELOPER

Wu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  Phyla_AMPHORA

:: MORE INFORMATION

Citation

Mol Biol Evol. 2013 Jun;30(6):1258-62. doi: 10.1093/molbev/mst059. Epub 2013 Mar 21.
A phylum-level bacterial phylogenetic marker database.
Wang Z1, Wu M.

AMPHORA2 – Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences

AMPHORA2

:: DESCRIPTION

AMPHORA is an automated phylogenomic inference application for large-scale protein phylogenetic analysis. It has been applied to automated genome tree construction and metagenomic sequence phylotyping.

::DEVELOPER

Wu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AMPHORA2

:: MORE INFORMATION

Citation

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.
Wu M1, Scott AJ.