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

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Maintainers


  • person_outline Debashish Bhattacharya <>
  • person_outline Ahmed Moustafa <>

Additional information


https://sourceforge.net/projects/phylosort

Publication for PhyloSort

PhyloSort in publications

 (6)
PMCID: 3998028
PMID: 24759094
DOI: 10.1038/srep04780

[…] 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 […]

PMCID: 3942023
PMID: 24448981
DOI: 10.1093/gbe/evu014

[…] 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 […]

PMCID: 3879968
PMID: 24259313
DOI: 10.1093/gbe/evt179

[…] 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 […]

PMCID: 3708498
PMID: 23645554
DOI: 10.1093/molbev/mst084

[…] 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 […]

PMCID: 2684587
PMID: 19484122
DOI: 10.1371/journal.pone.0005758

[…] synergistetes, thermotogae and verrucomicrobia). then phylogenies were inferred as described in the phylogenetic analyses (above) except alignments were refined using gblocks . finally, using phylosort , ml trees were grouped into different phylogenetic categories by matching topological criteria with at least 50% bootstrap support values, the topological criteria were defined to examine […]


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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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