Independence of alignment and tree search.
I assert that similarity is the appropriate homology criterion for sequence alignment, as it is with morphology. Methods that select among alignments using parsimony-based tree lengths, as implemented in MALIGN and POY, arrange the data such that they are consistent with a minimum-evolution model. When combining data sets in phylogenetic analyses, we are not trying to reinforce our earlier hypotheses about relationships, but rather to test them. The severity of this test is compromised when congruence with other characters is favored when selecting among alignment parameters.
Simmons
Mark P
MP
Department of Evolution, Ecology and Organismal Biology, The Ohio State University Herbarium, 1315 Kinnear Road, Columbus, OH 43212, USA. psimmons@lamar.colostate.edu
D000465:Algorithms; D001483:Base Sequence; D019143:Evolution, Molecular; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012984:Software