PhyloSift pipeline

PhyloSift specifications


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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  • person_outline Aaron E. Darling <>

Publication for PhyloSift

PhyloSift citations

PMCID: 5374222

[…] 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 (2, 3). genome completeness was estimated using phylosift, which revealed that each assembly contained single copies of 37 conserved single-copy marker genes (2). for all genomes, annotation was completed using rast (4). the results […]

PMCID: 4389573

[…] a k. pneumoniae concatenated marker gene maximum-likelihood tree was constructed using all available assembled k. pneumoniae genomes on the ncbi ftp server. the genomes were first processed with phylosift (darling et al., 2014) using –besthit and –isolate options to get alignments to concatenated conserved housekeeping genes. the tree was made using fasttree (price et al., 2010). the tree […]

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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