Section: Software and Platforms

Ancestral Genome Reconstructions

Participant : Eric Tannier.

• Contact: Eric Tannier (eric.tannier@inria.fr).

• We participated in the development of a series of softwares for genome organization analysis:

  • ANGES, for ANcestral GEnomeS maps, is a toolkit for ordering ancestral genomic markers in chromosomes. An application note has been published in Bioinformatics in 2012 to advertise its first release. It is hosted at SFU in Vancouver, URL: http://paleogenomics.irmacs.sfu.ca/ANGES/ , under a GNU license, 2012.

  • DeCo and DeCoLT, for Detection of Co-evolution (with Lateral gene Transfer), reconstruct neighborhood relationships between genes of ancient genomes, in the presence of gene duplications, transfer and losses. Both are hosted at the PRABI, the bioinformatics platform in Lyon, under a Cecill license, 2012 and 2013. URL: http://pbil.univ-lyon1.fr/software/DeCo/ and http://pbil.univ-lyon1.fr/software/DeCoLT/ .

  • DCJ2HP provides bayesian samples of rearrangements scenarios between two genomes. It is hosted at the Renyi Institute in Budapest. URL: http://www.renyi.hu/~miklosi/DCJ2HP/