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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

Subtools


  • CLIQUE
  • CONSENSE
  • CONTML
  • CONTRAST
  • DNACOMP
  • DNADIST
  • DNAINVAR
  • DNAML
  • DNAMLK
  • DNAMOVE
  • DNAPARS
  • DNAPENNY
  • DOLLOP
  • DOLMOVE
  • DOLPENNY
  • DRAWGRAM
  • DRAWTREE
  • FACTOR
  • FITCH
  • GENDIST
  • KITSCH
  • MIX
  • MOVE
  • NEIGHBOR
  • PARS
  • PENNY
  • PROML
  • PROMLK
  • PROTDIST
  • PROTPARS
  • RESTDIST
  • RESTML
  • RETREE
  • SEQBOOT
  • TREEDIST

Download


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Versioning


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Documentation


Publications for the PHYLogeny Inference Package

PHYLIP citations

 (3061)
library_books

Papain like and legumain like proteases in rice: genome wide identification, comprehensive gene feature characterization and expression analysis

2018
BMC Plant Biol
PMCID: 5952849
PMID: 29764367
DOI: 10.1186/s12870-018-1298-1

[…] le sequence alignments of amino acid sequences were performed using Clustal X ver. 1.81 with the default multiple alignment parameters. Phylogenetic tree was generated with Phylip Ver. 3.68 using the Protpars method. Protein sequences of papain-like and LLCPs from A. thaliana, H. vulgare and Z. mays were used in this analysis, and their accession numbers are listed in Additional file : Table S9 an […]

call_split

What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs

2018
PMCID: 5956146
PMID: 29743201
DOI: 10.1128/mSphere.00122-18
call_split See protocol

[…] 000 sequences ×100 times) (). Statistical analyses were done using an Adonis test with 999 permutations. A DNA distance maximum likelihood phylogenetic tree was constructed using the software package Phylip (). Representative sequences of the archaeal OTUs from the 16S rRNA gene data set were aligned with the complete 16S rRNA gene reference sequence database (RefSeq, NCBI, release 82) prefiltered […]

library_books

Widespread plant specialization in the polyphagous planthopper Hyalesthes obsoletus (Cixiidae), a major vector of stolbur phytoplasma: Evidence of cryptic speciation

2018
PLoS One
PMCID: 5940214
PMID: 29738577
DOI: 10.1371/journal.pone.0196969

[…] Amova) in Arlequin v.3.5.1.2 [].Genetic clustering and identity among H. obsoletus populations associated with the four host-plants were further inferred with a maximum-likelihood phenogram using the Contml algorithm in Phylip v.3.69 []. Hyalesthes luteipes individuals sampled on Ulmus minor in Serbia were used as an outgroup root. This analysis was based on four loci (F56, F84, H120, G85) that am […]

call_split

Genome wide analysis of the SPL/miR156 module and its interaction with the AP2/miR172 unit in barley

2018
Sci Rep
PMCID: 5935748
PMID: 29728569
DOI: 10.1038/s41598-018-25349-0
call_split See protocol

[…] SMART tool and are presented in Table . The phylogenetic tree was constructed using the maximum likelihood method using JTT + G as a best model. SBP domain amino acid sequences were converted to the PHYLIP format and analysed with the PhyML3.0 software (http://www.atgc-montpellier.fr/phyml/), which uses the approximate likelihood-ratio test (aLRT) and depends on a non-parametric Shimodaira-Hasega […]

call_split

The Xylella fastidosa RTX operons: evidence for the evolution of protein mosaics through novel genetic exchanges

2018
BMC Genomics
PMCID: 5935956
PMID: 29728072
DOI: 10.1186/s12864-018-4731-9
call_split See protocol

[…] ere then submitted to phylogenetic analysis using Phylip ver3.6 (distributed by the author, Felsenstein, J., Department of Genome Sciences, University of Washington, Seattle) and distance trees using Protdist and Fitch were determined. Protein distances were calculated using the Jones, Thornton, Taylor distance matrix []. The dotplot analysis was performed using Dotter in the ms dos environment [] […]

call_split

Dynamics of phosphorus and bacterial phoX genes during the decomposition of Microcystis blooms in a mesocosm

2018
PLoS One
PMCID: 5933731
PMID: 29723219
DOI: 10.1371/journal.pone.0195205
call_split See protocol

[…] n numbers of the gene sequences.The valid gene sequences obtained were compared using the MUSCLE program [], and the generated files in phylip format were analysed for nucleic acid distance using the DNAdist program []. The similarities in the generated files, as analysed, were compared by the Dotur program to acquire coverage (C), Chao 1 richness estimator (Schao), and the Shannon-Wiener index (H […]

Citations

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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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