Phylosift

Phylosift is a software tool for the phylogenetic analysis of genome and metagenome sequences to identify similar protein-coding and RNA sequences and thus potential homologs to a search sequence in a database. The Phylosift algorithm uses the Bayesian hypothesis guided by phylogeny. The Phylosift pipeline includes LAST, HMMER, and pplacer.

Topic

Metagenomics;Genomics

Detail

  • Operation: Phylogenetic tree analysis

  • Software interface: Command-line user interface;Suite

  • Language: Perl

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 1.0.1

  • Credit: The US Department of Homeland Security.

  • Input: -

  • Output: -

  • Contact: Aaron E. Darling aaron.darling@uts.edu.au

  • Collection: -

  • Maturity: -

Publications

  • PhyloSift: phylogenetic analysis of genomes and metagenomes.
  • Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ. 2014 Jan 9;2:e243.
  • https://doi.org/10.7717/peerj.243
  • PMID: 24482762
  • PMC: PMC3897386

Download and documentation

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