PhyloSift protocols

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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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Maintainer


  • person_outline Aaron E. Darling <>

Publication for PhyloSift

PhyloSift in pipelines

 (27)
2018
PMCID: 5867873
PMID: 29518047
DOI: 10.3390/genes9030152

[…] 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 […]

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

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

2017
PMCID: 5374222
PMID: 28360178
DOI: 10.1128/genomeA.00023-17

[…] on a paired-end 300-bp run of an illumina miseq. quality trimming error correction and assembly were performed using the a5-miseq assembly pipeline (, ). genome completeness was estimated using phylosift, which revealed that each assembly contained single copies of 37 conserved single-copy marker genes (). for all genomes, annotation was completed using rast (). the results […]

2017
PMCID: 5385130
PMID: 28396823
DOI: 10.7717/peerj.3134

[…] extracted using the ‘tree’ command in checkm. in checkm, open reading frames were called using prodigal v2.6.1 () and a set of 43 lineage-specific marker genes, similar to the universal set used by phylosift (), were identified and aligned using hmmer v3.1b1 (). initial phylogenetic analysis used pplacer (v1.1.alpha16-1-gf748c91) () to place sequences into a checkm tree/database (version 0.9.7) […]

2017
PMCID: 5418705
PMID: 28473000
DOI: 10.1186/s40168-017-0270-x

[…] the taxonomic annotations reported by checkm, we searched amino acid sequences for the reca gene for each mag in the national center for biotechnology information (ncbi) databases. we also used phylosift v1.0.1 [] to determine the phylogenomic relationships between our mags and a collection of 1758 reference genomes (with no redundancy at the species level) that we acquired from the ensembl […]


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PhyloSift in publications

 (103)
PMCID: 5943399
PMID: 29743478
DOI: 10.1038/s41398-018-0107-9

[…] 1, to access the assembly and richness of the microbiomial rna in blood, we used phylogenetic marker genes to assign the candidate microbial reads to the bacterial and archaeal taxa. we used phylosift (v 1.0.1 with default parameters) to perform taxonomic profiling of the whole blood samples. phylosift makes use of a set of protein coding genes found to be relatively universal (i.e., […]

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 […]

PMCID: 5867873
PMID: 29518047
DOI: 10.3390/genes9030152

[…] 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 […]

PMCID: 5787263
PMID: 29374496
DOI: 10.1186/s40168-018-0411-x

[…] 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 […]

PMCID: 5727513
PMID: 29235508
DOI: 10.1038/s41598-017-17640-3

[…] (~97%) were kept for further analysis (supplementary table ). a total of 145.8 million and 124.3 million filtered reads were obtained from the sediment and water samples respectively., kaiju and phylosift software were used to generate the taxonomic profile. in total, 21.78 million filtered reads of the “treatment” sediment dataset were assigned to the superkingdom level, accounting […]


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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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