PHYLUCE 1.5.0 – Software for UCE (and general) Phylogenomics

PHYLUCE 1.5.0

:: DESCRIPTION

phyluce (phy-loo-chee) is a software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes.

::DEVELOPER

faircloth-lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/Linux
  • Python

:: DOWNLOAD

 PHYLUCE

:: MORE INFORMATION

Citation

PHYLUCE is a software package for the analysis of conserved genomic loci.
Faircloth BC.
Bioinformatics. 2015 Nov 2. pii: btv646.

SuperTriplets 1.1 – Triplet-based Supertree Approach to Phylogenomics

SuperTriplets 1.1

:: DESCRIPTION

SuperTriplets is a triplet-based supertree approach to phylogenomics. It infers supertrees with branch support values.

::DEVELOPER

SuperTriplets team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 SuperTriplets

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jun 15;26(12):i115-23. doi: 10.1093/bioinformatics/btq196.
SuperTriplets: a triplet-based supertree approach to phylogenomics.
Ranwez V1, Criscuolo A, Douzery EJ.

SCI-PHY 3.01 – Subfamily Classification In PHYlogenomics

SCI-PHY 3.01

:: DESCRIPTION

SCIPHY is a software of tree construction and subfamily detection. It is the key downloadable code from the PhyloFacts repository.

::DEVELOPER

the Berkeley Phylogenomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  SCI-PHY

:: MORE INFORMATION

Citation

Automated protein subfamily identification and classification.
Brown DP, Krishnamurthy N, Sjölander K.
PLoS Comput Biol. 2007 Aug;3(8):e160.

forester 1.038 – Software Libraries for Phylogenomics and Evolutionary Biology Research

forester 1.038

:: DESCRIPTION

forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research.

::DEVELOPER

Christian M Zmasek

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 forester

:: MORE INFORMATION

Citation

Bioinformatics. 2001 Sep;17(9):821-8.
A simple algorithm to infer gene duplication and speciation events on a gene tree.
Zmasek CM, Eddy SR.

Phylemon 2.0 – Web-tools for Molecular Evolution, Phylogenetics, Phylogenomics and Hypothesis testing

Phylemon 2.0

:: DESCRIPTION

Phylemon is the suite of web-tools for molecular evolution, phylogenetics and phylogenomics. It is conceived as a natural response to the increasing demand of data analysis of experimental scientists seeking to add molecular evolution and phylogenetic insight into their research.

::DEVELOPER

Bioinformatics and Genomics Department at CIPF

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No, Only Web Service

:: MORE INFORMATION

Citation

Sánchez R, Serra F, Tárraga J, Medina I, Carbonell J, Pulido L, de María A, Capella-Gutíerrez S, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H.
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W470-4. Epub 2011 Jun 6.

SDM – Fast Distance-based Approach for (Super)Tree Building in Phylogenomics

SDM

:: DESCRIPTION

SDM (super distance matrix ) is a new method to combine distance matrices (or trees with branch lengths). This method involves deforming the different matrices, without modifying their topological message, to bring them as close as possible to each other. A distance supermatrix is then computed by averaging the deformed source matrices. When this supermatrix is complete, any tree building algorithm can be used to obtain the supertree that summarizes the input distance matrices (or trees with branch lengths); e.g. BioNJ or FastME (recommended).

::DEVELOPER

Alexis Criscuolo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

 SDM

:: MORE INFORMATION

Citation

SDM: a Fast Distance-based Approach for (Super)Tree Building in Phylogenomics.”
Criscuolo A., Berry V., Douzery E.J.P., Gascuel O.
Systematic Biology. 2006 55(5):740-755.

OrthoSelect – Selection of Orthologs in Phylogenomics

OrthoSelect

:: DESCRIPTION

OrthoSelect is a easy-to-install and easy-to-use tool for finding ortholog groups in EST databases. It automatically searches assembled EST sequences against databases of ortholog groups (OG), assigns ESTs to these pre-defined OGs, translates the sequences into proteins, eliminates redundant sequences assigned to the same OG, creates multiple sequence alignments of identified ortholog sequences and others the possibility to further process this alignment in a last step. OrthoSelect performes better than the best-hit selection strategy and shows reliable results re-annotating database member sequences of OrthoMCL-DB and KOG. Since a correct orthology assignment is a important prerequisite for the construction of reliable data sets, OrthoSelect is capable of producing such data sets. This makes a OrthoSelect a valuable tool for researcher dealing with large EST libraries focussing on constructing data sets for phylogenetic reconstructions.

::DEVELOPER

the Department of Bioinformatics of the University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OS X
  • Perl

:: DOWNLOAD

OrthoSelect

:: MORE INFORMATION

Citation

F. Schreiber, K. Pick, D. Erpenbeck, G. W?rheide, B. Morgenstern (2009)
OrthoSelect: a protocol for selecting orthologous groups in phylogenomics
BMC Bioinformatics 10, 219