PhiPack protocols

PhiPack computational protocol

PhiPack specifications


Unique identifier OMICS_21684
Name PhiPack
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability Stable
Source code URL
Maintained Yes


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  • person_outline Trevor Bruen <>

Publication for PhiPack

PhiPack IN pipelines

PMCID: 5844296
PMID: 29311113
DOI: 10.1534/g3.117.300316

[…] samples, with a custom python script. each sco was aligned using muscle 3.8.31(edgar 2004), and we consecutively tested each multiple sequence alignment (msa) for recombination using the software phipack (bruen and bruen 2005). an sco group was considered as not having signs of recombination if it passed all three tests run by phipack. then, nonrecombinant sco msas were polished with gblocks […]

PMCID: 5844296
PMID: 29311113
DOI: 10.1534/g3.117.300316

[…] whereas 4050 had all species represented, indicating the presence of a strong core set of genes., we retrieved 3408 scos, which were then aligned with muscle and tested for recombination with phipack. we retained 2147 nonrecombining scos and processed their msas with gblocks. the polished msas were concatenated obtaining an 870,212 bp long alignment. we used this final msa as input […]

PMCID: 5069460
PMID: 27756904
DOI: 10.1038/srep35045

[…] single-copy gene clusters were processed to generate a phylogenomic tree of all the organisms. first, all clusters were aligned using mafft65, and then checked for evidence of recombination using phipack66. a total of 275 clusters were selected, and all the alignments were concatenated. this large alignment matrix was trimmed using gblocks67, with a resulting alignment length of 202,423 nt. […]

PMCID: 4449606
PMID: 25880915
DOI: 10.1186/s12864-015-1476-6

[…] larger core gene datasets consisting of 1015 and 1046 single-copy genes present in all members of the "firm-5″ and “bifido″ groups, respectively. we applied three recombination-scanning methods in phipack (nss, maxchi and phi) on each alignment and found 89 genes with evidence of recombination in the “firm-5″ group (8.7%), while only 19 genes were significant for recombination in the “bifido” […]

PMCID: 3598968
PMID: 23289814
DOI: 10.1186/1471-2148-13-3

[…] each species as a separate population., because ima2 assumes no intragenic recombination or selection we tested each locus for recombination using the pairwise homoplasy index [83] implemented in phipack [84], and for selection performing multiple loci hka tests [85] using sites and hka [86]., to obtain a multilocus perspective of the diversification within the whole clade, we employed […]

PhiPack institution(s)
McGill Centre for Bioinformatics, McGill University, Montreal, QC, Canada; Program in Evolutionary Biology, Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, Montreal, QC, Canada; Department of Mathematics, University of Auckland, Auckland, New Zealand
PhiPack funding source(s)
Supported by the National Science Engineering and Research Council (NSERC) (postgraduate scholarship B); Le Fonds quebecois de la recherche sur la nature et les technologies (FQRNT grant 2003-NC- 81840); the NSERC (grant 238975-01).

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