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Protocols

Bio::Phylo specifications

Information


Unique identifier OMICS_23504
Name Bio::Phylo
Software type Application/Script
Interface Command line interface, Application programming interface
Restrictions to use None
Input format NEWICK,NEXUS,NeXML,CSV,FASTA,PHYLIP,TSV,PhyloXML,NHX,FASTQ/RDF
Output format NEWICK,NEXUS,NeXML,CSV,FASTA,PHYLIP,TSV,PhyloXML,NHX,FASTQ/RDF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
License Artistic License version 2.0, GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Download


download.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Rutger Vos

Additional information


https://github.com/rvosa/bio-phylo/blob/master/lib/Bio/Phylo/Manual.pod

Publications for Bio::Phylo

Bio::Phylo citations

 (13)
library_books

Non Human Primates Harbor Diverse Mammalian and Avian Astroviruses Including Those Associated with Human Infections

2015
PLoS Pathog
PMCID: 4646697
PMID: 26571270
DOI: 10.1371/journal.ppat.1005225

[…] was computed using the `phylocurve_perm`R library, and that library's internal sampling procedures were used for rarefaction. UniFrac and MMCC were computed using a custom python script utilizing the Bio.Phylo library. Within this script, each focus community of sequences was rarefied by random sub-sampling of tree tips using python's random.sample function. UniFrac and MMCC metrics were then comp […]

call_split

Coordinated Evolution of Influenza A Surface Proteins

2015
PLoS Genet
PMCID: 4527594
PMID: 26247472
DOI: 10.1371/journal.pgen.1005404
call_split See protocol

[…] er of background mutations is preserved.All procedures for construction of constrained gene trees were implemented in C++ with bio++ package [,]. Mapping of mutations was implemented in Perl and used Bio::Phylo package []. […]

call_split

Intrasubtype Reassortments Cause Adaptive Amino Acid Replacements in H3N2 Influenza Genes

2014
PLoS Genet
PMCID: 3886890
PMID: 24415946
DOI: 10.1371/journal.pgen.1004037
call_split See protocol

[…] than one lineage on the phylogeny were categorized as parallel, and replacements that reverted to a once-ancestral state, reversing.All manipulations with phylogenetic trees were done using the Perl Bio::Phylo package . The statistical analyses were performed with R . […]

library_books

Snf2 Family Gene Distribution in Higher Plant Genomes Reveals DRD1 Expansion and Diversification in the Tomato Genome

2013
PLoS One
PMCID: 3842944
PMID: 24312269
DOI: 10.1371/journal.pone.0081147

[…] Data preparation, conversion and filtering were performed with custom Perl scripts, BioPerl [] and Bio::Phylo []. For the Snf2 gene calling in potato, potato protein sequences were determined by aligning all candidate Snf2 ATPase protein sequences against the potato genome using tBlastn [] (E-value […]

library_books

Structural and evolutionary adaptation of rhoptry kinases and pseudokinases, a family of coccidian virulence factors

2013
BMC Evol Biol
PMCID: 3682881
PMID: 23742205
DOI: 10.1186/1471-2148-13-117

[…] ma model of rate variation, empirically estimated amino acid frequencies and 100 bootstrap runs, taking the output of FastTree as the user-supplied starting tree. Finally, we used script based on the Bio.Phylo module of Biopython [] to reroot the tree with ePK as the outgroup, collapse all splits with less than 25% bootstrap support, colorize the specific clades of interest and visualize the tree. […]

call_split

Population dynamics of rhesus macaques and associated foamy virus in Bangladesh

2013
PMCID: 3675400
PMID: 26038465
DOI: 10.1038/emi.2013.23
call_split See protocol

[…] lt from the entire gag nucleic acid sequence alignment using FastTree v2.1.3 with a Jukes–Cantor model. The tips of this tree were colored by sampling location using a python script together with the Bio.Phylo Biopython library. This colored tree was rendered using Archaeopteryx v0.957 beta (http://www.phylosoft.org/archaeopteryx/). Additionally, a NeighborNet splits network was constructed using […]

Citations

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Bio::Phylo institution(s)
Naturalis Biodiversity Center, Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
Bio::Phylo funding source(s)
Supported by the European Community’s Seventh Framework Programme (FP7/2007- 2013) under grant agreement no. 237046.

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