DeCo - Evolution of gene neighborhoods

A more recent implementation of DeCo called DeCoSTAR, get it here.

It includes the original DeCo algorithm with transfer, boltzmann sampling, and other various options.

The software DeCo computes adjacencies (or any type of relation, like regulation, interaction, functional relationships) between ancestral genes from gene phylogenies reconciled with a species phylogeny according to duplications and losses. It takes as input (1) a species tree (2) a set of extant genes (3) a set of exant adjacencies (relations) between extant genes and (4) gene trees which leaves are the extant genes. It outputs ancestral species, genes, and adjacencies. It also highlights the duplications involving several genes.

It is distributed under Cecill open source Licence.

The algorithm is described in Bérard et al, Evolution of gene neighborhoods within reconciled phylogenies published in Bioinformatics special online issue dedicated to the ECCB 2012 proceedings.

The supplementary text, with proofs and additional discussions, can be found here

For the software, use the following links:

Get DeCo

Use DeCo

Page hosted by the PRABI and LBBE, Last modification July 2012

Contact: Severine dot Berard at univ-montp2 dot fr, or Eric dot Tannier at inria dot fr