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. W...

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Bibliographic Details
Published in:Molecular phylogenetics and evolution 2004-06, Vol.31 (3), p.874-879
Main Author: Simmons, Mark P.
Format: Article
Language:English
Subjects:
Algorithms
Base Sequence
Evolution, Molecular
Likelihood Functions
Molecular Sequence Data
Phylogeny
Sequence Analysis, DNA
Software
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Summary: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.
ISSN:1055-7903
1095-9513
DOI:10.1016/j.ympev.2003.10.008