Genome-scale evolution: reconstructing gene orders in the ancestral species, Genome Research, vol.12, issue.1, pp.26-36, 2002. ,
Multiple Genome Rearrangement and Breakpoint Phylogeny, Journal of Computational Biology, vol.5, issue.3, pp.555-570, 1998. ,
DOI : 10.1089/cmb.1998.5.555
On the PATHGROUPS approach to rapid small phylogeny, BMC Bioinformatics, vol.12, issue.Suppl 1, 2011. ,
DOI : 10.1186/1471-2105-12-S1-S4
Reconstructing Ancestral Gene Orders Using Conserved Intervals, Lecture Notes in Computer Science, vol.3240, pp.14-25, 2004. ,
DOI : 10.1007/978-3-540-30219-3_2
Reconstructing contiguous regions of an ancestral genome, Genome Research, vol.16, issue.12, pp.1557-1565, 2006. ,
DOI : 10.1101/gr.5383506
Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study, Genome Biology, vol.8, issue.11, p.236, 2007. ,
DOI : 10.1186/gb-2007-8-11-r236
A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes, PLoS Computational Biology, vol.48, issue.11, p.1000234, 2008. ,
DOI : 10.1371/journal.pcbi.1000234.t003
URL : https://hal.archives-ouvertes.fr/inria-00269397
Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes, Bioinformatics, vol.26, issue.8, pp.1119-1121, 2010. ,
DOI : 10.1093/bioinformatics/btq079
Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution, Journal of Computational Biology, vol.14, issue.4, pp.436-445, 2007. ,
DOI : 10.1089/cmb.2007.A005
A flexible ancestral genome reconstruction method based on gapped adjacencies, BMC Bioinformatics, vol.13, 2012. ,
ANGES: reconstructing ANcestral GEnomeS maps, Bioinformatics, vol.28, issue.18, pp.2388-2390, 2012. ,
DOI : 10.1093/bioinformatics/bts457
URL : https://hal.archives-ouvertes.fr/hal-00733180
Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology, Systematic Zoology, vol.20, issue.4, pp.406-416, 1971. ,
DOI : 10.2307/2412116
Minimal Mutation Trees of Sequences, SIAM Journal on Applied Mathematics, vol.28, issue.1, pp.35-42, 1975. ,
DOI : 10.1137/0128004
Recovering genome rearrangements in the mammalian phylogeny, Genome Research, vol.19, issue.5, pp.934-942, 2009. ,
DOI : 10.1101/gr.086009.108
Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II, Journal of Computational Biology, vol.17, issue.9, pp.1097-1112, 2010. ,
DOI : 10.1089/cmb.2010.0092
URL : https://hal.archives-ouvertes.fr/hal-00681091
Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs, Genome Research, vol.18, issue.11, pp.1814-1828, 2008. ,
DOI : 10.1101/gr.076554.108
Ensembl Genomes: Extending Ensembl across the taxonomic space, Nucleic Acids Research, vol.38, issue.Database, pp.563-569, 2010. ,
DOI : 10.1093/nar/gkp871
The NCBI Taxonomy database, Nucleic Acids Research, vol.40, issue.D1, pp.136-143, 2012. ,
DOI : 10.1093/nar/gkr1178
URL : http://doi.org/10.1093/nar/gkr1178
Reconstructing the architecture of the ancestral amniote genome, Bioinformatics, vol.27, issue.19, pp.2664-2671, 2011. ,
DOI : 10.1093/bioinformatics/btr461
URL : https://hal.archives-ouvertes.fr/hal-00698104
Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution, BMC Evolutionary Biology, vol.9, issue.1, 2009. ,
DOI : 10.1186/1471-2148-9-84
URL : http://doi.org/10.1186/1471-2148-9-84