Gene tree parsimony for incomplete gene trees: addressing true biological loss.

We present new theory for GTP considering whether the incompleteness is due to gene birth and death (i.e., true biological loss) or taxon sampling, and present dynamic programming algorithms that can be used for an exact but exponential time solution for small numbers of taxa, or as a heuristic for larger numbers of taxa. We also prove that the "standard" calculations for duplications and losses exactly solve GTP when incompleteness results from taxon sampling, although they can be incorrect when incompleteness results from true biological loss. The software for the DP algorithm is freely available as open source code at https://github.com/smirarab/DynaDup. PMID: 29387142 [PubMed]
Source: Algorithms for Molecular Biology : AMB - Category: Molecular Biology Authors: Tags: Algorithms Mol Biol Source Type: research