Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference.

ABSTRACT: In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the sco

SUBMITTER: Chernomor O 

PROVIDER: S-EPMC4663649 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature