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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). Java Development Kit version 1.4.2 minimum.

JAVA

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ISEM

A C++ shell program to detect co-evolving groups of sites CoMap performs the following tasks: - Compute probabilistic substitution maps - Test for pairs/groups of sites that do not evolve independently

C++

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ecceTERA: Tree Estimating using Reconciliation and Amalgamation
version 1.2.4, 14/09/2016
(formerly known as TERA)


Given a (dated) species tree S, a set of gene trees G, and a set of costs for gene events (duplications, transfers and losses), ecceTERA computes the score of a most parsimonious reconciliation (MPR).
Additionally, ecceTERA will also compute either:

(1) a reconciliation graph describing all reconciliations for the species tree and each tree in G, according to the combinatorial model defined in [1], as well as the median reconciliations [3] and a random reconciliation (each reconciliation is outputted along with its score and event supports supports [3]), or (2) an MPR score for the “amalgamation” of all the gene trees in G (considered as unrooted), as well as an optimal gene tree according to the combinatorial model defined in [2].


[1] Celine Scornavacca, Wojciech Paprotny and Vincent Berry and Vincent Ranwez. Journal of Bioinformatics and Computational Biology Vol. 11, No. 2 (2013), p. 1250025.
[2] Celine Scornavacca, Edwin Jacox, and Gergely Szöllősi. Joint Amalgamation of Most Parsimonious Reconciled Gene Trees. Bioinformatics (2014): btu728.
[3] Thi-Hau Nguyen, Vincent Ranwez, Vincent Berry, Celine Scornavacca. Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods. PloS One Vol. 8, No. 10 (2013), p. e73667.

C++

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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.

C++

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ISEM

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.

C++

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ISEM