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boussau documents
Science
How to use PHYLDOG: a tutorial
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Gene tree-species tree methods in RevBayes
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Presentation describing ALE, a suite of programs for gene tree reconstruction in the presence of gene duplication, transfer and loss
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Evolutionary genomics
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Towards inferring the history of life in the presence of lateral gene transfers. Evolution 2014
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Genome-scale phylogenomics
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Models of gene duplication, transfer and loss to study genome evolution