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
>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