01993nas a2200241 4500008004100000245006200041210006000103260000800163300001200171490000700183520137700190653002401567653000801591653001401599653000801613653001501621653001801636653000801654653001601662653001401678100001801692856004101710 2005 eng d00aDirect optimization, affine gap costs, and node stability0 aDirect optimization affine gap costs and node stability cSEP a641-6530 v363 aThe 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.10adirect optimization10adna10aevolution10agap10amorphology10aphylogenetics10apoy10asensitivity10astability1 aAagesen, Lone u__://000231591500017__