Simultaneous Bayesian gene tree reconstruction and reconciliation analysis, Proceedings of the National Academy of Sciences, vol.106, issue.14, pp.5714-5719, 2009. ,
DOI : 10.1073/pnas.0806251106
Phylogenetic and Functional Assessment of Orthologs Inference
Projects and Methods, PLoS Computational Biology, vol.19, issue.1, p.1000262, 2009. ,
DOI : 10.1371/journal.pcbi.1000262.s018
Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution, Proceedings of the eighth annual international conference on Computational molecular biology , RECOMB '04, pp.326-335, 2004. ,
DOI : 10.1145/974614.974657
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss, Bioinformatics, vol.28, issue.12, pp.283-291, 2012. ,
DOI : 10.1093/bioinformatics/bts225
Van de Peer. The gain and loss of genes during 600 million years of vertebrate evolution, Genome Biol, pp.7-43, 2006. ,
Jane: a new tool for the cophylogeny reconstruction problem, Algorithms for Molecular Biology, vol.5, issue.1, p.16, 2010. ,
DOI : 10.1186/1748-7188-5-16
Rapid evolutionary innovation during an Archaean genetic expansion, Nature, vol.15, issue.7328, pp.93-96, 2011. ,
DOI : 10.1038/nature09649
DTLS-trees: proving the parsimony model for reconciling gene and species trees, 2012. ,
Models, algorithms and programs for phylogeny reconciliation, Briefings in Bioinformatics, vol.12, issue.5, pp.392-400, 2011. ,
DOI : 10.1093/bib/bbr045
URL : https://hal.archives-ouvertes.fr/lirmm-00825041
An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers, Research in Computational Molecular Biology: Proceedings of the 14th International Conference on Research in Computational Molecular Biology, pp.93-108, 2010. ,
DOI : 10.1007/978-3-642-16181-0_9
URL : https://hal.archives-ouvertes.fr/lirmm-00818889
A Hybrid Micro???Macroevolutionary Approach to Gene Tree Reconstruction, Journal of Computational Biology, vol.13, issue.2, pp.320-335, 2006. ,
DOI : 10.1089/cmb.2006.13.320
Inferring Evolutionary Scenarios in the Duplication, Loss and Horizontal Gene Transfer Model, Logic and Program Semantics, pp.83-105, 2012. ,
DOI : 10.1007/978-3-642-29485-3_7
Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution, Genome Biology, vol.8, issue.7, p.141, 2007. ,
DOI : 10.1186/gb-2007-8-7-r141
From Gene Trees to Species Trees, SIAM Journal on Computing, vol.30, issue.3, pp.729-752, 2000. ,
DOI : 10.1137/S0097539798343362
A parameter-adaptive dynamic programming approach for inferring cophylogenies, BMC Bioinformatics, vol.11, issue.Suppl 1, p.60, 2010. ,
DOI : 10.1186/1471-2105-11-S1-S60
Accounting for gene tree uncertainty improves gene tree accuracy as well as duplications, transfers and losses predictions, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01189848
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations, Proceedings of the National Academy of Sciences, 2012. ,