Downloads

Baobab is an editor for large phylogenetic trees written in Java. ree editor means that it allows you to create and/or modify a tree interactively, adding/(re)moving branches and nodes, changing leave names, setting parameters. Baobab focuses on edition, not representation and display that are only used as a tool to make edition easier. arge means that Baobab includes tools to simplify the task of managing heavy dataset (typically dealing with several hundred species).

Julien Dutheil

3.31

Linux - Windows

Yes

0

R-package program to detect markers responding to selection.

Renaud VITALIS

0.8

Linux - Windows - Mac

Yes

0

GENCLONE is designed for studying clonality and its spatial components using genotype data with molecular markers from haploid or diploid organisms.

Arnaud-Haond Sophie and Belkhir Khalid

2.0

Windows

No

0

Genepop is a population genetics software package originally developed by Michel Raymond and Francois Rousset, at the Laboratiore de Genetique et Environment, Montpellier, France. Genepop runs under Windows, and can also be compiled to run under Unix or Linux. It will compile on Mac OSX machines if you have the developer tools installed.

François Rousset

4.0

Linux - Windows - Mac

Yes

0

Set of population genetics programs

Khalid Belkhir

4.05

Windows

No

0

Given a dated species tree S and a gene tree G, this program computes the graph reconciliation for G and S, according to the combinatorial model defined in [Celine Scornavacca, Wojciech Paprotny and Vincent Berry and Vincent Ranwez. Vol. 11, No. 2 (2013) 1250025 (19 pages) Journal of Bioinformatics and Computational Biology].

This work was partially supported by the IBC http://www.ibc-montpellier.fr/

Céline Scornavacca

1

Linux

Yes

0

Phylogenetic reconstruction

Bio++

HGT_simul implements the phylogenomic simulation procedure described in: Galtier N. 2007. A model of horizontal gene transfer and the bacterial phylogeny problem. Systematic Biology (in press) The underlying model incorporates horizontal gene transfers between lineages, gene tree depth, genome-wide or gene-specific departure from the molecular clock, across-site rate variation, and various nucleotide or amino-acid substitution processes. The user can also control the geometry of the data set: number of taxa, number of genes, sequence lengths, and sampling effort. The input is a (rooted) species tree + an option file setting the parameters of the simulation. The output is a set of genes; for each gene, the simulated alignement and the underlying true gene tree are written in separate files.

Galtier N.

1.2

Linux - Windows - Mac

Yes

0

ISEM

Permutation test of relatedness

Belkhir K, Castric V, Bonhomme F.

1.1

Windows

No

0

ISEM

Estimating divergence time on population trees from dense SNP data: a Bayesian model based on Kimura diffusion equations.

Gautier, Vitalis

1

Linux

No

0

Build biological populational model

Jean-Baptiste Ferdy

1.0

Linux

Yes

0

NEW MACSE version (1.01b)

MACSE now provides a full toolkit dedicated to coding sequence alignments. This toolkit allows us to reliably align thousands of COI and matK sequences in a barcoding context (see our barcoding subproject web page for further information). Here are some of the functionalities provided by the various subprograms included in MACSE: Enriching an existing alignment with additional sequences Refining an existing alignment Splitting an existing alignment keeping a subset of sites and/or sequences Formatting and exporting an alignment (e.g. by removing or masking codons containing frameshifts) Translating a nucleotide alignment into an amino acid alignment ... For usage examples see MACSE tutorial and download associated examples.
Source code of MACSE can be downloaded, using the svn facilities of redmine with the following command line and "guest" as login and password: svn checkout http://kimura.univ-montp2.fr/svn/macse
project web page: MACSE Webpage

corresponding author: vincent.ranwez@supagro.inra.fr

Vincent RANWEZ, Sebastien HARISPE, Frederic DELSUC, Emmanuel DOUZERY

1.01b

Linux - Windows - Mac

Yes

0

Alignment

Migraine implements coalescent algorithms for maximum likelihood analysis of population genetic data. The version available through this page implements only a limited set of models, as described in Rousset and Leblois (2007): essentially a simple model of isolation by distance in a linear habitat, including the island model as a sub-case. The data handled are allelic counts.

François Rousset and Raphaël Leblois

2.0

Linux

Yes

0

ISEM

Monolocus Neutrality Test

Khalid Belkhir and François Bonhomme

1.0

Windows

No

0

Partition is a model-based statistical software package for identifying population sub-division and assigning individuals to populations, on the basis of their genotypes at co-dominant marker loci. The underlying population genetic model is appropriate for out-crossing diploid organisms.

Khalid Belkhir and Kevin J. Dawson

2.0

Windows

No

0

ISEM

PartitionML is a program that searches for the best possible partition of a sample into independent panmictic clusters and simultaneously assign individuals to them using a maximum likelihood (ML) criterion.

Khalid Belkhir and François Bonhomme

1

Windows

No

0

ISEM