PhyloSift is a suite of software tools to conduct phylogenetic analysis of genomes and metagenomes.
Using a reference database of protein sequences, PhyloSift can scan new sequences against that database for homologs and identify the phylogenetic relationship of the new sequence to the database sequences. During this procedure, high quality alignments of codon and
amino acid sequence are generated.
Software Download on GitHub: https://github.com/gjospin/PhyloSift
Google Group for user support: https://groups.google.com/d/forum/phylosift
PhyloSift has several new features :
- The marker gene database is being expanded to encompass Bacteria, Archaea, Eukarya, and virii.
- Support for processing of next-gen sequence data including Illumina, 454, and others
- Integration with metAMOS for pre-assembling next-generation datasets
- Codon based alignment of marker genes
…more to come!
Darling AE, Jospin G, Lowe E, Matsen FA IV, Bik HM et al. (2014) PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e243 http://dx.doi.org/10.7717/peerj.243
LICENSE AND COPYRIGHT
PhyloSift is copyright (C) 2011 Aaron Darling and Guillaume Jospin
This program is free software; you can redistribute it and/or modify it under the terms of either: the GNU General Public License as published by the Free Software Foundation.
THIRD PARTY SOFTWARE
PhyloSift is distributed with several open source components that were developed by other groups. These components are (c) their respective developers and are redistributed with PhyloSift to provide ease-of-use.
Please see the following web sites for licensing details and source code for these other components:
* pplacer — http://matsen.fhcrc.org/pplacer/
* rapsearch2 — http://omics.informatics.indiana.edu/mg/RAPSearch2/
* HMMER 3 — http://hmmer.janelia.org/
* LAST — http://last.cbrc.jp
* pda — http://www.cibiv.at/software/pda/
* bowtie2 — http://bowtie-bio.sourceforge.net/bowtie2/
* FastTree — http://www.microbesonline.org/fasttree/
* infernal — http://infernal.janelia.org/
Please direct correspondence to aaron (dot) darling (at) uts (dot) edu (dot) au