A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences.
We have developed a rapid parsimony method for reconstructing ancestral nucleotide states that allows calculation of initial branch lengths that are good approximations to optimal maximum-likelihood estimates under several commonly used substitution models. Use of these approximate branch lengths (rather than fixed arbitrary values) as starting points significantly reduces the time required for iteration to a solution that maximizes the likelihood of a tree. These branch lengths are close enough to the optimal values that they can be used without further iteration to calculate approximate maximum-likelihood scores that are very close to the "exact" scores found by iteration. Several strategies are described for using these approximate scores to substantially reduce times needed for maximum-likelihood tree searches.
Rogers
J S
JS
Department of Biological Sciences, University of New Orleans, New Orleans, Louisiana 70148, USA. jsrbs@uno.edu
Swofford
D L
DL
D000818:Animals; D001483:Base Sequence; D002816:Chordata, Nonvertebrate; D004247:DNA / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D003663:Decision Trees; D016013:Likelihood Functions; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics; D012044:Regression Analysis; D015203:Reproducibility of Results
D004275:DNA, Ribosomal; D012335:RNA, Ribosomal; D004247:DNA