PHYLIP protocols

PHYLIP specifications

Information


Unique identifier OMICS_04240
Name PHYLIP
Alternative name the PHYLogeny Inference Package
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format Text Only, flat ASCII
Output format NEWICK
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
Computer skills Advanced
Version 3.696
Stability Stable
Maintained Yes

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Documentation


Publications for the PHYLogeny Inference Package

PHYLIP IN pipelines

 (180)
2018
PMCID: 5803895
PMID: 29415704
DOI: 10.1186/s12896-017-0412-z

[…] species had e values tens of orders of magnitude lower than viral proteins., amino acid alignments were automatically generated using clustalx2 [23] and manually corrected, as required. protdist (phylip version 3.695) was used to generate distance matrices with the jones-taylor-thornton model. unrooted trees were then generated using the neighbor-joining method (neighbor; phylip package) […]

2018
PMCID: 5803895
PMID: 29415704
DOI: 10.1186/s12896-017-0412-z

[…] required. protdist (phylip version 3.695) was used to generate distance matrices with the jones-taylor-thornton model. unrooted trees were then generated using the neighbor-joining method (neighbor; phylip package) and drawn using the phylip drawtree postscript generator., the assembled sf-rvn cell genome comprised 392 mb in 66,319 contigs at approximately 121-fold coverage, and the assembled […]

2018
PMCID: 5803895
PMID: 29415704
DOI: 10.1186/s12896-017-0412-z

[…] was used to generate distance matrices with the jones-taylor-thornton model. unrooted trees were then generated using the neighbor-joining method (neighbor; phylip package) and drawn using the phylip drawtree postscript generator., the assembled sf-rvn cell genome comprised 392 mb in 66,319 contigs at approximately 121-fold coverage, and the assembled sf-rvn cell transcriptome comprised […]

2018
PMCID: 5873417
PMID: 29330904
DOI: 10.1002/ps.4859

[…] between treatment types using the minitab 17 mintab.com, coventry, uk. cv3 2te statistical package., phylogenetic analysis was performed as described previously7 using the phylogeny package phylip.16 clustalw was used to align multiple full‐length protein sequences, the distance measure between paired sequences was computed using prodist, and the umgma option in neighor was used to used […]

2018
PMCID: 5917017
PMID: 29725343
DOI: 10.3389/fpls.2018.00503

[…] agriculture research system (cars-12)., http://articles.extension.org/pages/61006 , http://afsmseq.sourceforge.net/ , http://vcftools.sourceforge.net/ , http://evolution.genetics.washington.edu/phylip.html , http://tree.bio.ed.ac.uk/software/figtree/ , https://cran.r-project.org/package=pheatmap , the supplementary material for this article can be found online at: […]

PHYLIP institution(s)
Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Radiological Sciences, University of Puerto Rico School of Medicine, San Juan, Puerto Rico, USA; Georgia Institute of Technology, Atlanta, GA, USA
PHYLIP funding source(s)
This work was funded by the United States National Institutes of Health National Institute of General Medical Sciences grant No. 2 T36GM008789, the Pittsburgh Supercomputing Center National Resource for Biomedical Supercomputing funded through the United States National Institutes of Health National Center for Research Resources grant 2 P41 RR06009, the United States National Institutes of Health through the National Center for Research Resources, the United States National Science Foundation through TeraGrid.

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