PhyloSift protocols

PhyloSift specifications

Information


Unique identifier OMICS_10429
Name PhyloSift
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Aaron E. Darling <>

Publication for PhyloSift

PhyloSift IN pipelines

 (6)
2018
PMCID: 5804319
PMID: 29423345
DOI: 10.7717/peerj.4320

[…] (‘read recruitment’ is an analogous term to ‘mapping’, or ‘short read alignment’). we used samtools (li et al., 2009) to convert resulting sam files into sorted and indexed bam files., we used phylosift v1.0.1 (darling et al., 2014) with default parameters to quantify evolutionary distances between genomes. briefly, phylosift (1) identifies a set of 37 marker gene families in each genome, […]

2017
PMCID: 5331489
PMID: 28183779
DOI: 10.1128/genomeA.01307-16

[…] out as described by liu et al. (6). vizbin was used to extract the metagenomic bins from the metagenome contigs, using default settings (7). contigs shorter than 2,000 bp were removed from each bin. phylosift (8) and jspeciesws (9) were used to determine the phylogenetic affiliation of each bin. the completeness, contamination rate, and average amino acid index (aai) were calculated […]

2017
PMCID: 5615132
PMID: 28959738
DOI: 10.1128/mSphere.00277-17

[…] (table 2). mags with an estimated completeness level lower than 50% were not included in this study., a total of 19 mags were classified in the verrucomicrobia phylum based on taxonomic assignment by phylosift using 37 conserved phylogenetic marker genes (64), as described by bendall et al. (37). a phylogenetic tree was reconstructed from the 19 verrucomicrobia mags and 25 reference genomes using […]

2016
PMCID: 4918448
PMID: 26744812
DOI: 10.1038/ismej.2015.241

[…] table s7., genomes were classified based on the taxonomic assignments from a subset of 37 conserved marker genes, mostly ribosomal proteins, extracted from the reconstructed genomes using phylosift (darling et al., 2014). marker genes with cumulative probability masses <0.80 were removed. genomes were assigned to the finest taxonomic scale for which all marker genes agreed, ranging […]

2016
PMCID: 4918448
PMID: 26744812
DOI: 10.1038/ismej.2015.241

[…] was assigned to the tm7 phylum through phylogenetic analysis of marker genes from previously published tm7 genomes. marker genes in other tm7 genomes were identified and concatenated using phylosift, and a maximum likelihood tree was generated using raxml with the dayhoff substitution model (supplementary figure s6; stamatakis, 2014). bootstraps were generated with 100 replicates using […]

PhyloSift institution(s)
ithree institute, University of Technology Sydney, Sydney, Australia; Genome Center, University of California, Davis, CA, USA; Department of Evolution and Ecology, University of California, Davis, CA, USA; Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA; Fred Hutchinson Cancer Research Center, Seattle, WA, USA
PhyloSift funding source(s)
US Department of Homeland Security contract HSHQDC-11-C-00091

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