phylip package question

joe at removethispart.gs.washington.edu joe at removethispart.gs.washington.edu
Sun Oct 20 16:28:16 EST 2002


In article <aos956$40n$1 at mercury.hgmp.mrc.ac.uk>,
Chris Hoffmann  <choffman at lucas.cis.temple.edu> wrote:
>i saw that DNADIST saved the dist matrixes for the data sets that were
>analyzed (that is: they did not have bootstrapped sequences that yielded
>infinite distances) on the output file, up to the moment the program found a
>data set with infinitely distant sequences.
>them i used other bootstrap sets to run DANDIST and append the result to the
>previous file, in the end i had around the number of replicates i wanted
>(haven't had the time yet to see if the resulting consensus tree makes sense
>or not).
>lots of work, but i couldn't think of any other way to go around it.
>so here is my question:

It would probably bias your results toward putting the species
close together.

It is hard to know what to do about all this.

-- 
Joe Felsenstein         joe at removethispart.gs.washington.edu
 Department of Genome Sciences, University of Washington,
 Box 357730, Seattle, WA 98195-7730 USA
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