This is a list of softwares to which I contributed with other authors. Most of them are available on the ATGC bioinformatic platform. Web forms are also available there to run software online on our servers.

Building Supertrees

Ancestral Build - v1 and MLS: multi-layer supertree - v0.8 written in Java 1.4. The first is a fast polynomial time algorithm to decide the ancestral compatibility of source trees with internal labels, eg displaying higher-level taxa such as genuses, orders, families. See (Berry & Semple, Syst Biol 06). The program is provided with a graphical interface written with the Jung library that shows the progressive decomposition of the descendancy graph. MLS is a heuristic optimization algorithm to compute a supertree for a set of compatible or incompatible source trees with internal labels (Berry et al, to be submitted). It uses SplitsTree v3 and the MascOpt library. Both Ancestral Build and MLS are available as compressed archives.

PhySIC: Phylogenetic Signal with Induction and non-Contradiction: a veto supertree method for supertree inference. Online web server. Program also available for download. (Ranwez et al Syst Biol 2007).

PhySIC_IST: cleaning source trees to infer more informative supertrees: a flexible supertree method that can adopt a broad scale of behaviours from vote to veto when handling topological conflict between input trees. The method also has the advantage of detecting anomalies in each source tree wrt the rest of the collection. This suggests horizontal transfers or reconstruction artefacts such as long branch attraction. Online web server with graphical interface to compare source trees in order to interpret incongruences in the source trees. Program also available for download. (Scornavacca et al BMC Bioinformatics 2008).

Comparing trees

ScriptTree a tool to graphically visualize topological differences between trees and to display annotations wrt parts of phylogenies. See Experimental Web Site. (Chevenet et al to be submitted soon).

PhyloExplorer a tool to manage and query phylogeny collections and find related published phylogenies. Two versions are available depending on the reference taxonomy: NCBI or or ITIS (Ranwez et al, in revision for BMC Bioinformatics).

Program MPC: Multi-Polar Consensus: a program implementing the consensus method described in (Bonnard, Berry & Lartillot, Syst Biol 06) : given a set of phylogenies on the same data set, the idea is to summarize this collection as a set of bipartitions embedded in a small number of trees, rather than in just one tree, as done usually. This allows for the representation of alternative phylogenetic signal otherwise lost due to the compatibility constraint of output bipartitions. Available for download

Program of the FPT algorithm for computing the Maximum Agreement Subtree (MAST) of rooted trees described in (Berry & Nicolas CPM 04, TCBB 06). Available on request from the first author. See (de Vienne et al 07, von Haeseler et al 08, de Vienne et al 08) for a use of this program in a procedure to obtain a congruency index between two topologies. Associated web site.

Program of the linear-time 3-approximation algorithm for computing the MAST of rooted trees described in (Berry et al COCOON 05, TALG 09). Available on request from the first author.

Reconstructing phylogenies from quartets

• Several algorithms I contributed with Dave Bryant and Charles Semple are implemented in the current version of SplitsTree: a must-have program in phylogenetics! (Berry & Bryant 99, Bryant & Berry 01, Berry & Semple 06).


Package PHYLOQUART v1.3: exact and heuristic methods (Phylip compatible). Program of the algorithms in (Berry & Gascuel COCOON 96, TCS 00), (Berry & Bryant RECOMB 99, Bryant & Berry Adv Appl Math 01) Available for download

• Global Cleaning v1.0 (40k) : correcting wrong quartets. Program of an algorithm in (Berry et al ESA 99) Available for download