TY - JOUR T1 - Direct optimization, affine gap costs, and node stability JF - Molecular Phylogenetics and Evolution Y1 - 2005 A1 - Aagesen, Lone SP - 641 EP - 653 KW - direct optimization KW - dna KW - evolution KW - gap KW - morphology KW - phylogenetics KW - poy KW - sensitivity KW - stability AB - The outcome of a phylogenetic analysis based on DNA sequence data is highly dependent on the homology-assignment step and may vary with alignment parameter costs. Robustness to changes in parameter costs is therefore a desired quality of a data set because the final conclusions will be less dependent on selecting a precise optimal cost set. Here, node stability is explored in relationship to separate versus combined analysis in three different data sets, all including several data partitions. Robustness to changes in cost sets is measured as number of successive changes that can be made in a given cost set before a specific clade is lost. The changes are in all cases base change cost, gap penalties, and adding/removing/changing affine gap costs. When combining data partitions, the number of clades that appear in the entire parameter space is not remarkably increased, in some cases this number even decreased. However, when combining data partitions the trees from cost sets including affine gap costs were always more similar than the trees were from cost sets without affine gap costs. This was not the case when the data partitions were analyzed independently. When data sets were combined similar to 80% of the clades found under cost sets including affine gap costs resisted at least one change to the cost set. (c) 2005 Elsevier Inc. All rights reserved. VL - 36 UR - ://000231591500017 N1 - PDFTimes Cited: 0ArticleEnglishCited References Count: 57960lh ER -