Sequence alignments -- where to chop?

Joe Felsenstein joe at evolution.genetics.washington.edu
Tue Apr 23 01:15:37 EST 1996

In article <1996Apr18.105053 at ebi.ac.uk>,  <higgins at ebi.ac.uk> wrote:
>I could be wrong but ....
>as long as you cut the same section out of all the sequences, you actually
>protect yourself from these "violations".   The classic violation is to
>break the so called triangle inequality. 

There are few phylogeny methods that care one way or the other about the
Triangle Inequality.  Even though the things mathematicians call a "distance"
must satisfy it, the things that are used in distance matrix methods don't
have to.   The Distance Wagner method is one that does need it, but it is not
in wide use.  All other methods basically don't care about it.

Joe Felsenstein         joe at genetics.washington.edu     (IP No.
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

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