Nov 212014

TERA 1.0


Given a dated species tree S, a set of gene trees G, and a set of costs for gene events (duplications, transfers and losses), TERA computes the score of a most parsimonious reconciliation (MPR).


Institut des Sciences de l’Evolution de Montpellier (ISEM)




  • Linux
  • C++ Compiler





Joint Amalgamation of Most Parsimonious Reconciled Gene Trees.
Scornavacca C, Jacox E, Szöllősi GJ.
Bioinformatics. 2014 Nov 6. pii: btu728.

Nov 212014
BoolNet 2.0.1 - Generation,Reconstruction and analysis of Boolean networks

BoolNet 2.0.1 :: DESCRIPTION BoolNet is an R package for the generation, reconstruction, simulation and analysis of Boolean networks ::DEVELOPER Medical Systems Biology, University of Ulm :: SCREENSHOTS N/A :: REQUIREMENTS Linux/ Mac OsX/ Windows R package :: DOWNLOAD  BoolNet :: MORE INFORMATION Citation Bioinformatics. 2010 May 15;26(10):1378-80. doi: 10.1093/bioinformatics/btq124. Epub 2010 Apr 7. BoolNet–an R [...]

Nov 212014
MetExplore 2.4 - Web Server to Link Metabolomic Experiments and Genome-scale Metabolic Networks

MetExplore 2.4 :: DESCRIPTION MetExplore is a web server to link metabolomic experiments and genome-scale metabolic networks. ::DEVELOPER MetExplore Team :: SCREENSHOTS N/A :: REQUIREMENTS Web Browser :: DOWNLOAD  NO :: MORE INFORMATION Citation Nucleic Acids Res. 2010 Jul;38(Web Server issue):W132-7. doi: 10.1093/nar/gkq312. Epub 2010 May 5. MetExplore: a web server to link metabolomic experiments and [...]

Nov 212014
Blast2GO 2.8 - Functional Annotation Tool

Blast2GO 2.8 :: DESCRIPTION Blast2GO® is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. ::DEVELOPER The Genomics of Gene Expression Lab :: SCREENSHOTS :: REQUIREMENTS Linux/Windows/MacOsX Java :: DOWNLOAD  Blast2GO :: MORE INFORMATION Citation A. Conesa, S. Götz, J. M. Garcia-Gomez, J. Terol, M. Talon and M. Robles. [...]

Nov 212014
ngKLAST 4.5 - Exploration of Biological Sequence Databanks and related Information

ngKLAST 4.5 :: DESCRIPTION ngKLAST  is an all-in-one KLAST and BLAST workstation to produce quickly and efficiently high-quality results out of any kind of sequences: proteins, genes, reads, contigs, metagenomes, etc. ::DEVELOPER Korilog SARL :: SCREENSHOTS :: REQUIREMENTS Windows/ Linux / Mac OsX JAVA :: DOWNLOAD  ngKLAST :: MORE INFORMATION

Nov 212014
ASAP 1.4.1 - A Systematic Annotation Package for Community Analysis of Genomes

ASAP 1.4.1 :: DESCRIPTION ASAP is designed to organize the data associated with a genome from the early stages of sequence annotation through genetic and biochemical characterization, providing a vehicle for ongoing updates of the annotation and a repository for genome-scale experimental data. ::DEVELOPER Genome Evolution Laboratory :: SCREENSHOTS N/A :: REQUIREMENTS Windows/ Linux / [...]

Nov 212014
Utopia Documents 2.4.4- Tool for Interacting with the Scientific Literature

Utopia Documents 2.4.4 :: DESCRIPTION Utopia Documents is a novel tool for interacting with the scientific literature. Utopia Documents allows new ways of thinking about your documents: it brings your papers to life by linking to live resources on the web and turning static data into live interactive content. ::DEVELOPER The University of Manchester :: SCREENSHOTS [...]

Nov 212014
Mauve 2.3.1 - Multiple Genome Alignments

Mauve 2.3.1 :: DESCRIPTION Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics on a new scale. Aligning whole genomes is a fundamentally different problem [...]

Nov 202014
flowDensity 1.1.0 - Sequential Flow Cytometry Data Gating

flowDensity 1.1.0 :: DESCRIPTION flowDensity facilitates reproducible, high-throughput analysis of flow cytometry data by automating a predefined manual gating approach. ::DEVELOPER M. Jafar Taghiyar, Mehrnoush Malek <mmalekes at> :: SCREENSHOTS N/A :: REQUIREMENTS Linux / Windows/ MacOsX R BioConductor :: DOWNLOAD  flowDensity :: MORE INFORMATION Citation Bioinformatics. 2014 Oct 16. pii: btu677. flowDensity: reproducing manual [...]

Nov 202014
motifanalysis 0.1.1 - Motif Analysis

motifanalysis 0.1.1 :: DESCRIPTION motifanalysis allows the search of motifs with binding sites enriched in particular genomic regions. ::DEVELOPER IZKF Computational Biology and Bioinformatics Research Group :: SCREENSHOTS N/A :: REQUIREMENTS Linux Python :: DOWNLOAD  motifanalysis :: MORE INFORMATION