AMPHORA
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 the 2nd version AMPHORA2 can be read here. AMPHORA is open source. The current version can be downloaded from github
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 7,542 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.
A paper describing can be found here. 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 here Phyla_AMPHORA.tar.gz.
A paper describing the original AMPHORA can be read here. A paper describing the 2nd version AMPHORA2 can be read here. AMPHORA is open source. The current version can be downloaded from github
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 7,542 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.
A paper describing can be found here. 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 here Phyla_AMPHORA.tar.gz.
Zorro
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.
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.
PhyloCore
PhyloCore is an application that uses a phylogeny-based algorithm to identify the core microbiota taxa at the proper taxonomic levels.
A paper describing the software can be found here.
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.
A paper describing the software can be found here.
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.
