Exabayes: Massively parallel bayesian tree inference for the whole-genome era, Molecular biology and evolution, vol.31, issue.10, pp.2553-2556, 2014. ,
Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative, Systematic biology, vol.55, issue.4, pp.539-552, 2006. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00136658
Lvb: parsimony and simulated annealing in the search for phylogenetic trees, Bioinformatics, vol.20, issue.2, pp.274-275, 2004. ,
Two c++ libraries for counting trees on a phylogenetic terrace, Bioinformatics, 2018. ,
Consequences of common topological rearrangements for partition trees in phylogenomic inference, Journal of Computational Biology, vol.22, issue.12, pp.1129-1142, 2015. ,
Terrace aware data structure for phylogenomic inference from supermatrices, Systematic biology, vol.65, issue.6, pp.997-1008, 2016. ,
The state of software for evolutionary biology, Molecular biology and evolution, vol.35, issue.5, pp.1037-1046, 2018. ,
Computational complexity of inferring phylogenies from dissimilarity matrices, Bulletin of Mathematical Biology, vol.49, issue.4, pp.461-467, 1987. ,
The prevalence of terraced treescapes in analyses of phylogenetic data sets, BMC evolutionary biology, vol.18, issue.1, p.46, 2018. ,
Confidence limits on phylogenies: an approach using the bootstrap, Evolution, vol.39, issue.4, pp.783-791, 1985. ,
Bionj: an improved version of the nj algorithm based on a simple model of sequence data, Molecular biology and evolution, vol.14, issue.7, pp.685-695, 1997. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00730410
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of phyml 3.0. Systematic biology, vol.59, pp.307-321, 2010. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00511784
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Systematic biology, vol.52, issue.5, pp.696-704, 2003. ,
Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees, BMC bioinformatics, vol.12, issue.1, p.470, 2011. ,
Using raxml-ng in practice, Phylogenetics in the Genomic Era, 2020. ,
URL : https://hal.archives-ouvertes.fr/hal-02535311
The bayesian approach to molecular phylogeny, Phylogenetics in the Genomic Era, 2020. ,
URL : https://hal.archives-ouvertes.fr/hal-02535330
Phylobayes: Bayesian phylogenetics using site-heterogeneous models, Phylogenetics in the Genomic Era, 2020. ,
URL : https://hal.archives-ouvertes.fr/hal-02535342
Phynav: A novel approach to reconstruct large phylogenies, Classification-the Ubiquitous Challenge, pp.386-393, 2005. ,
Renewing felsenstein's phylogenetic bootstrap in the era of big data, Nature, vol.556, issue.7702, p.452, 2018. ,
URL : https://hal.archives-ouvertes.fr/lirmm-02078445
Ultrafast approximation for phylogenetic bootstrap, Molecular biology and evolution, vol.30, issue.5, pp.1188-1195, 2013. ,
Phylogenomics resolves the timing and pattern of insect evolution, Science, vol.346, issue.6210, pp.763-767, 2014. ,
Increasing the Efficiency of Searches for the Maximum Likelihood Tree in a Phylogenetic Analysis of up to 150 Nucleotide Sequences, Systematic Biology, vol.56, issue.6, pp.988-1010, 2007. ,
Iq-tree: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Molecular biology and evolution, vol.32, issue.1, pp.268-274, 2015. ,
The parsimony ratchet, a new method for rapid parsimony analysis, Cladistics, vol.15, issue.4, pp.407-414, 1999. ,
Awty (are we there yet?): a system for graphical exploration of mcmc convergence in bayesian phylogenetics, Bioinformatics, vol.24, issue.4, pp.581-583, 2008. ,
fastdnaml: a tool for construction of phylogenetic trees of dna sequences using maximum likelihood, Bioinformatics, vol.10, issue.1, pp.41-48, 1994. ,
How many bootstrap replicates are necessary, Journal of computational biology, vol.17, issue.3, pp.337-354, 2010. ,
Comparison of phylogenetic trees, Mathematical biosciences, vol.53, issue.1-2, pp.131-147, 1981. ,
A short proof that phylogenetic tree reconstruction by maximum likelihood is hard, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), vol.3, issue.1, p.92, 2006. ,
Mrbayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space, Systematic biology, vol.61, issue.3, pp.539-542, 2012. ,
Rec-i-dcm3: A fast algorithmic technique for reconstructing large phylogenetic trees, Proc. 3rd IEEE Computational Systems Bioinformatics Conf. CSB" 04, pp.98-109, 2004. ,
, Impacts of terraces on phylogenetic inference, 2014.
Terraces in phylogenetic tree space, Science, vol.333, issue.6041, pp.448-450, 2011. ,
Tree-puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing, Bioinformatics, vol.18, issue.3, pp.502-504, 2002. ,
Consel: for assessing the confidence of phylogenetic tree selection, Bioinformatics, vol.17, issue.12, pp.1246-1247, 2001. ,
An efficient program for phylogenetic inference using simulated annealing, Parallel and Distributed Processing Symposium, 2005. Proceedings. 19th IEEE International, p.8, 2005. ,
Phylogenetic search algorithms for maximum likelihood, Computational Molecular Biology: Techniques, Approaches and Applications, pp.547-577, 2011. ,
Raxml version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, issue.9, pp.1312-1313, 2014. ,
Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data, Bioinformatics, vol.26, issue.12, pp.132-139, 2010. ,
A rapid bootstrap algorithm for the raxml web servers, Systematic biology, vol.57, issue.5, pp.758-771, 2008. ,
, Paup*: Phylogenetic analysis using parsimony, 2001.
Accelerated likelihood surface exploration: the likelihood ratchet, Systematic Biology, vol.52, issue.3, pp.368-373, 2003. ,
GARLI, vers. 0.951. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion, 2006. ,