Bio::Phylo statistics

Tool stats & trends

Looking to identify usage trends or leading experts?


Bio::Phylo specifications


Unique identifier OMICS_23504
Name Bio::Phylo
Software type Application/Script
Interface Command line interface, Application programming interface
Restrictions to use None
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




No version available



  • person_outline Rutger Vos

Additional information

Publications for Bio::Phylo

Bio::Phylo citations


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

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 […]


Coordinated Evolution of Influenza A Surface Proteins

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 []. […]


Intrasubtype Reassortments Cause Adaptive Amino Acid Replacements in H3N2 Influenza Genes

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 . […]


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

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 […]


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

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. […]


Population dynamics of rhesus macaques and associated foamy virus in Bangladesh

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 ( Additionally, a NeighborNet splits network was constructed using […]


Looking to check out a full list of citations?

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.

Bio::Phylo reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Bio::Phylo