Publications - Working papers

Please find below working papers of our group. Currently, we list 42 working papers. In the list are only not published papers present. If you look for a preprint of an already published paper you must look in the "Published papers" section. If you have problems accessing electronic information, please let us know:

©NOTICE: All working papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

Split-Inducing Indels in Phylogenomic Analysis

Alexander Donath, Peter F. Stadler

Download


[ PDF ]  [ Software ]

Abstract


Most phylogenetic studies using molecular data treat gaps in multiple sequence alignments as missing data or even completely exclude alignment columns that contain gaps. Here we show that gap patterns in large-scale, genome-wide alignments are themselves phylogenetically informative and can be used to infer reliable phylogenies provided the gap data are properly filtered to reduce noise introduced by the alignment method. We introduce here the notion of split-inducing indels (splids) that define an approximate bipartition of the taxon set. We show both in simulated data and in case studies on real-life data that splids can be efficiently extracted from phylogenomic data sets. They provide a surprisingly clear phylogenetic signal and lead to quite accurate phylogenetic

Keywords


in/del, splits, genome-wide multiple sequence alignments, phylogenomics,