Tools : Phylogeny and comparative genomics
| Name | Platform | Description | Link | |
 |
ape | R-package for Analyses of Phylogenetics and Evolution | CRAN - package ape | |
| AthGInRel | Toulouse |
Allows to penetrate inside the Arabidopsis genome for studying the inter-relation which exist for each genes (duplication alone, multigenic family). | software info | |
|
BAOBAB | Montpellier |
editor for large phylogenetic trees | homepage |
|
BCG | Toulouse |
bacterian genomic comparative tools | BCG online |
| BioNJ | OUEST-genopole Pasteur Paris Bordeaux Montpellier |
a version of the NJ algorithm improved for molecular sequences | online form | |
| Cassis | PRABI |
methods for precise detection of genomic rearrangement breakpoints | Download Cassis | |
| dnadist | Lille |
Program to compute distance matrix from nucleotide sequences | online form | |
| dnapars | Lille |
DNA Parsimony Program | online form | |
|
DT-SCORE | Montpellier |
a distance based tandem duplication tree reconstruction algorithm. | webpage |
| fastDNAml | Pasteur Paris Bordeaux |
Construction of phylogenetic trees of DNA sequences using maximum likelihood | online form | |
|
FastMe | OUEST-genopole Montpellier |
A very fast and accurate phylogeny software | FastME Web Page |
|
Figenix | Marseille |
automates complex pipelines of phylogenetic analysis, gene prediction and EST analysis under the supervision of an expert system | Figenix server |
|
GAME | Montpellier |
Efficient biased estimation of evolutionary distances when substitution rates vary across sites. | website |
|
Homolens | PRABI |
a database of homologous genes from Ensembl fully sequenced organisms, it allows one to visualize multiple alignments and phylogenetic trees. | Homolens homepage |
|
Iccare | Toulouse |
comparative sequence analysis, mapping information and primer/overgo design | Iccare’s homepage |
|
IMGT/PhyloGene | Montpellier |
Tool for immunoglobulin and T cell receptor variable gene sequences. | IMGT/PhyloGene online |
|
JaDis | PRABI |
A program for computing distances between nucleic acid sequences. | Jadis homepage |
| list of tree softwares | A comprehensive list of tree-softwares for visualisation and manipulations | List | ||
|
NARCISSE | Toulouse |
Browser of compared genomes | Narcisse online |
| neighbor | Lille Pasteur Paris |
Neighbor-Joining and UPGMA methods | online form | |
|
NHML | PRABI Montpellier |
a package inluding programs for maximum-likelihood phylogenetic inferences from DNA sequence data using a non-homogeneous Markov model of DNA sequence evolution. | webpage |
|
NJplot | PRABI |
A tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format | NJplot homepage |
|
Phydbac | Marseille |
a web interactive tool that display phylogenomic profiles of bacterial protein sequences | Phydbac online |
| PHYLIP | Lille Pasteur Paris Bordeaux |
Phylogeny Inference Package | online in Bordeaux | |
|
PhyloJava | PRABI |
A client/server tool dedicated to phylogenetic tree reconstruction. | webpage |
|
Phylo_win | PRABI Montpellier |
A graphical colour interface for molecular phylogenetic inference. | Phylo_win’s homepage |
|
PhyML | Montpellier |
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood | PhyML online |
|
Principal coordinates analysis | PRABI |
a method for building sequence ordinations using sets of aligned sequences | |
| protdist | Lille Pasteur Paris Bordeaux |
Program to compute distance matrix from protein sequences | online form in Lille | |
|
Q* | Montpellier |
A collection of programs aimed at estimating phylogenies from a quartet principle. | webpage |
|
QR2 | Montpellier |
a reduction algorithm for approximating a (nonmetric) dissimilarity by a tree distance | QR2 online |
|
RAP | PRABI |
Phylogenetic Tree Reconciler | webpage |
|
RRTree | PRABI |
Program for relative-rate tests. | webpage |
| SWEEP-BOTT | Montpellier |
A program dedicated to the detection of bottlenecks and selective-sweeps from a coalescence-based maximum-likelihood analysis of DNA sequence polymorphism data. | Sweep bott homepage | |
| TreeGen | OUEST-genopole |
Tree generation from distance data. | TreeGen online | |
|
Unrooted | PRABI |
Tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format. | webpage |
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