LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites |
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Authors: | Liat Shavit Grievink David Penny Mike D Hendy Barbara R Holland |
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Affiliation: | (1) The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11 222, Palmerston North, New Zealand |
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Abstract: | Background Commonly used phylogenetic models assume a homogeneous evolutionary process throughout the tree. It is known that these homogeneous models are often too simplistic, and that with time some properties of the evolutionary process can change (due to selection or drift). In particular, as constraints on sequences evolve, the proportion of variable sites can vary between lineages. This affects the ability of phylogenetic methods to correctly estimate phylogenetic trees, especially for long timescales. To date there is no phylogenetic model that allows for change in the proportion of variable sites, and the degree to which this affects phylogenetic reconstruction is unknown. |
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