PhyloSort statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PhyloSort
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Tool usage distribution map

This map represents all the scientific publications referring to PhyloSort per scientific context
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Protocols

PhyloSort specifications

Information


Unique identifier OMICS_22627
Name PhyloSort
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data Some phylogenetic trees.
Output data Trees with matching monophyletic clades.
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.3
Stability Stable
Maintained Yes

Download


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Versioning


No version available

Maintainers


  • person_outline Debashish Bhattacharya
  • person_outline Ahmed Moustafa

Additional information


https://sourceforge.net/projects/phylosort

Publication for PhyloSort

PhyloSort citations

 (10)
call_split

PhySortR: a fast, flexible tool for sorting phylogenetic trees in R

2016
PeerJ
PMCID: 4868591
PMID: 27190724
DOI: 10.7717/peerj.2038
call_split See protocol

[…] in is also considered as the support for the opposing bacterial clade (Proteobacteria + Cyanobacteria) on the tree. This is distinct from the assumption of the lowest common ancestor for a clade in PhyloSort (), in which subtree-rooting could be invoked during a search.Existing utilities identify clades of interest without considering the occurrence of the target leaves elsewhere on the tree. Fo […]

library_books

SICLE: a high throughput tool for extracting evolutionary relationships from phylogenetic trees

2016
PeerJ
PMCID: 5012314
PMID: 27635331
DOI: 10.7717/peerj.2359

[…] HGT between co-occurring extremophilic bacteria and archaea () or HGT of cyanobacterial origin into the genomes of green algae (). Several programs have implemented similar search processes including PhyloSort (), Pyphy (), PhyloGenie () and most recently PhySortR (). However, in order to identify and summarize multiple evolutionary signals in a set of gene trees (e.g., all putative cases of HGT, […]

library_books

Single cell genome analysis of an uncultured heterotrophic stramenopile

2014
Sci Rep
PMCID: 3998028
PMID: 24759094
DOI: 10.1038/srep04780

[…] selected, aligned via MAFFT v641, and used for phylogenetic reconstruction under the PROTGAMMALG evolutionary model of RAxML v.7.2.830. The resulting trees were sorted for patterns of monophyly using PhyloSort. A multi-protein alignment of length 25,143 amino acids was produced by sampling our in-house database for homologs to the 458 CEGs. Each individual CEG family was aligned with its MAST-4 pe […]

library_books

Horizontal Gene Transfer and Redundancy of Tryptophan Biosynthetic Enzymes in Dinotoms

2014
Genome Biol Evol
PMCID: 3942023
PMID: 24448981
DOI: 10.1093/gbe/evu014

[…] lementary file S2, Supplementary Material online). RAxML 7.2.8 () was run to reconstruct the phylogenetic trees, with LG substitution matrix + Γ4 + F evolutionary model with 100 bootstrap replicates. PhyloSort () was used to cluster the repetitive phylogenetic trees for the queries with multiple paralogs. The 49 reconstructed phylogenies divided into four clusters corresponding to the four protein […]

library_books

Horizontal Gene Transfer is a Significant Driver of Gene Innovation in Dinoflagellates

2013
Genome Biol Evol
PMCID: 3879968
PMID: 24259313
DOI: 10.1093/gbe/evt179

[…] ellate species were also removed because monophyly could not be assessed and to mitigate any potential signal from contamination. For each tree, dinoflagellate nearest neighbors were identified using Phylosort, a tool for sorting phylogenetic trees by searching for a user-specified grouping of interest (). For this analysis, a nearest neighbor association is defined as a sister relationship betwee […]

library_books

Genome Analysis of Elysia chlorotica Egg DNA Provides No Evidence for Horizontal Gene Transfer into the Germ Line of This Kleptoplastic Mollusc

2013
Mol Biol Evol
PMCID: 3708498
PMID: 23645554
DOI: 10.1093/molbev/mst084

[…] ansferred algal genes (). This was based on Basic Local Alignment Search Tool (BLAST) analysis against the nonredundant National Center for Biotechnology Information (NCBI) database and also by using Phylosort, a phylogenomic pipeline designed to identify candidates of gene transfer (). Although a handful of putatively transferred genes (mostly of bacterial or viral origin) emerged from these anal […]


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PhyloSort institution(s)
University of Iowa, Interdisciplinary Program in Genetics, Iowa City, IA, USA; University of Iowa, Department of Biological Sciences and the Roy J. Carver Center for Comparative Genomics, Iowa City, IA, USA
PhyloSort funding source(s)
Supported by a grant from the National Institutes of Health (R01ES013679).

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