parsimony algorithms

Joe Felsenstein joe at evolution.genetics.washington.edu
Mon Dec 1 11:41:51 EST 1997

In article <65f24u$a7i at net.bio.net>,
jeroen witteveldt  <jeroenw at lx.student.wau.nl*REMOVETHIS*> wrote:
>I recently heard somebody say the parimony algorithm PAUP uses is better
>than the algorithme Phylip (3.572c) uses. Because I don't own a
>Macintosh I 
>rather use Phylip then PAUP.  
>Can somebody tell me the differences between both programs, especially
>differences when using both for bootstrapping? 

PAUP is *much* faster, and does a more thorough search for most
parsimonious tree.  Thus it can run bootstrap replicates much faster.
However since the error measured by bootstrapping tends to be very large
compared to the error made by not searching precisely for the most
parsimonious tree, it may not matter to the result.

Joe Felsenstein         joe at genetics.washington.edu
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

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