Bio::Phylo statistics

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Associated diseases

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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

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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

library_books

BMC Bioinformatics
PMCID: 3056726
PMID: 21352572
DOI: 10.1186/1471-2105-12-63

Bio::Phylo in publications

 (7)
PMCID: 4527594
PMID: 26247472
DOI: 10.1371/journal.pgen.1005404

[…] 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 []., to infer positive epistasis between mutations at two sites mapped onto the same phylogeny, we employ the method previously described in []. briefly, for each pair of sites […]

PMCID: 3886890
PMID: 24415946
DOI: 10.1371/journal.pgen.1004037

[…] 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 ., we thank mikhail roytberg for discussion of the reassortments mapping algorithm, and sergey kryazhimskiy, joshua plotkin, […]

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

[…] information was obtained from the tree-of-life project (http://tolweb.org/) and phytozome. , 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 [] […]

PMCID: 3353162
PMID: 22502588
DOI: 10.1186/1748-7188-7-6

[…] value of x with respect to  t  can be computed in polynomial time. in fact, an algorithm with run time o(n2) is presented in []. an implementation of this algorithm is available as part of the bio::phylo software package []., in [] the index hed was introduced which is defined as follows. let p : x → [0, 1] be a map that assigns to each x ∈ x a real number in the closed interval between 0 […]

PMCID: 3359215
PMID: 22443110
DOI: 10.1186/1471-2180-12-43

[…] (reviewed in []). however, a common flexible framework for their joint application in specialized phylogenetic studies and mlsa in general is still required. the bioperl libraries, including the bio::phylo package [,], provide valuable tools for the automation of analyses, but the connections between different steps are often not automated, making them time-consuming. unus allows […]


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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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