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.

A paper describing the original AMPHORA can be read here.

A paper describing AMPHORA2 can be read here AMPHORA2.pdf

The user manual for AMPHORA2 can be read here AMPHORA2 User Manual.pdf

AMPHORA is open source. The current version can be downloaded from github

Last update 07/15/13.


ZORRO is a probabilistic masking program that accounts for uncertainty in protein sequence alignments. It assigns a confidence score to each column in the alignment that can be used for alignment masking and trimming.

A paper describing the software can be read here.

ZORRO is open source. A readme file, the source code and executables can be downloaded here.


QuickES is a wrapper program for the Ecotype Simulation Algorithm that can predict ecotypes based on DNA sequences alone. QuickES sacrifices some of the precision of the complete algorithm in exchange for dramatically increased speed. QuickES is capable of analyzing tens of thousands of sequences.

A readme file and the source code can be downloaded


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.

The user manual for Phyla_AMPHORA can be read here Phyla_AMPHORA User Manual.pdf.

Phyla_AMPHORA is open source. The source code can be downloaded from github. If you download the source code from github, you also need to download the phylogenetic marker database (Marker.tar.gz) and put it in the Phyla_AMPHORA folder. Alternatively, you can download the entire package Phyla_AMPHORA.tar.gz  (the md5 checksum 7b21c364f1d30c7df66c21c37896e9b5).

Last update 03/19/13.

PhyloCore is an application that uses a phylogeny-based algorithm to identify the core microbiota taxa at the proper taxonomic levels.

Two flavors of PhyloCore are provided. One in python  and  one in perl. The python version works in both Unix/Linux and Mac. The perl version only works in Unix/Linux. You can download them here.