PHYLIP pipeline

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 citations

 (69)
2018
PMCID: 5873417

[…] 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 […]

2017
PMCID: 5686800

[…] [23]. evolutionary analyses of 16s rrna sequences were carried out using clustalw (version 2.1) to multiple aligned sequences. the maximum-likelihood phylogenetic tree was then constructed using phylip (version 3.695) [24] with the bootstrap algorithm set to 500, and the phylogenetic tree was visualized using figtree (version 1.4.3) (http://tree.bio.ed.ac.uk/software/fgtree/)., […]

2017
PMCID: 5325327

[…] universally present among sequenced genomes was obtained using the muscle alignment program [41]. this sequence alignment was used to estimate genetic distances using protdist from j. felsenstein’s phylip phylogeny inference package program [42]. on the basis of these estimated distances, successive clustering of lineages was performed using a neighbor-joining algorithm reported by zhang […]

2016
PMCID: 5358717

[…] atcc 17924), were used to construct the phylogenetic tree, along with mdr-shh02. briefly, multiple sequence alignment was performed using clustalw-2.1 (22). subsequently, the software package phylip 3.695 (http://evolution.genetics.washington.edu/phylip.html), along with the bootstrap algorithm, was used to construct the maximum likelihood phylogenetic tree, and the phylogenetic tree […]

2016
PMCID: 5138195

[…] all clusters were aligned with muscle (edgar, 2004) and then concatenated together. we performed phylogenetic analysis using a neighbor-joining algorithm with 1,000 bootstraps implemented in the phylip package., all reads with average quality values below 15 were discarded. the reads were truncated at 3′-end and first 25 bases were used for mapping. the reads were mapped to the m. […]

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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