title: A new support measure to quantify the impact of local optima in phylogenetic analyses.
abstract: Phylogentic analyses are often incorrectly assumed to have stabilized to a single optimum. However, a set of trees from a phylogenetic analysis may contain multiple distinct local optima with each optimum providing different levels of support for each clade. For situations with multiple local optima, we propose p-support which is a clade support measure that shows the impact optima have on a final consensus tree. Our p-support measure is implemented in our PeakMapper software package. We study our approach on two published, large-scale biological tree collections. PeakMapper shows that each data set contains multiple local optima. p-support shows that both datasets contain clades in the majority consensus tree that are only supported by a subset of the local optima. Clades with low p-support are most likely to benefit from further investigation. These tools provide researchers with new information regarding phylogenetic analyses beyond what is provided by other support measures alone.
authors: Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843, USA.
authors: Grant
authors: G
authors: Brammer
authors: Seung-Jin
authors: SJ
authors: Sul
authors: Tiffani L
authors: TL
authors: Williams