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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

Versioning


No version available

Documentation


Maintainer


  • person_outline Aaron E. Darling

Publication for PhyloSift

PhyloSift citations

 (119)
library_books

Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia

2018
PMCID: 5943399
PMID: 29743478
DOI: 10.1038/s41398-018-0107-9

[…] ng our filtering pipeline, an average of 33,546 of 100,000 unmapped reads are identified as high quality, unique non-host reads and were used as candidate microbial reads in our analyses. From these, PhyloSift was able to assign an average of 1235 reads (1.24 ± 0.41%, mean ± standard deviation) to the bacterial and archaeal gene families. A total of 1880 taxa were assigned, with 23 taxa at the phy […]

library_books

GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan Genome Phylogenies, Used for a Critical Geno Taxonomic Revision of the Genus Stenotrophomonas

2018
Front Microbiol
PMCID: 5938378
PMID: 29765358
DOI: 10.3389/fmicb.2018.00771

[…] developed and benchmarked GET_PHYLOMARKERS, an open-source, comprehensive, and easy-to-use software package for phylogenomics and microbial genome taxonomy. Programs like amphora (Wu and Eisen, ) or phylosift (Darling et al., ) allow users to infer genome-phylogenies from huge genomic and metagenomic datasets by scanning new sequences against a reference database of conserved protein sequences to […]

library_books

Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain)

2018
Genes
PMCID: 5867873
PMID: 29518047
DOI: 10.3390/genes9030152

[…] omes or bins. Further refinement of bins was carried out with VizBin v0.9 []. Their taxonomic affiliation was determined by constructing a genomic tree with FastTree v2.1.3 [] of the concatenation of PhyloSift v.1.0.1 [] set of conserved genes from the extracted bins and reference genomes obtained from National Center for Biotechnology Information (NCBI) Refseq database. Average nucleotide identit […]

library_books

Chronic Rhinosinusitis: Potential Role of Microbial Dysbiosis and Recommendations for Sampling Sites

2018
PMCID: 5836553
PMID: 29541629
DOI: 10.3389/fcimb.2018.00057

[…] Sequences were demultiplexed with Phylosift 1.0.1 (Darling et al., ) and merged using FLASh 1.2.11 (Magoc and Salzberg, ) with default settings, except for a minimum overlap of 80 and maximum of 140 bases. Merged sequences were qualit […]

call_split

Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid Cayman Rise reveals new insights into metabolism and diversity

2018
Microbiome
PMCID: 5787263
PMID: 29374496
DOI: 10.1186/s40168-018-0411-x
call_split See protocol

[…] and functions of contigs of bins identified as bacterial as well as to create GenBank files that contain the location and amino acid sequence of genes identified in each genome. We used the pipeline phylosift_v1.0.1 [] using “phylosift all” with the –isolate and –besthit flags to confirm the taxonomic assignation of the identified draft genomes. RNAmmer 1.2 Server (http://www.cbs.dtu.dk/services/ […]

library_books

Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses

2018
Microbiome
PMCID: 5748958
PMID: 29291746
DOI: 10.1186/s40168-017-0383-2

[…] sequences from duplicate samples were pooled and subsequently used for phylogenetic assessment (based on 37 single copy phylogenetic gene markers in addition to 16S rRNA and 18S rRNA genes) using the Phylosift pipeline []. Briefly, the analysis through the Phylosift pipeline involved searching sequences for identity to a known database of reference gene families, alignment to reference multiple al […]

Citations

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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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