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DNA vs amino acid sequences

Joe Felsenstein joe at evolution.genetics.washington.edu
Mon Jun 26 16:12:22 EST 1995

In article <DEernisse-2506951545380001 at deernisse.fullerton.edu>,
Doug Eernisse <DEernisse at fullerton.edu> wrote:
>In article <ts15-2306951442190001 at>, ts15 at cornell.edu (Ted
>Schultz) wrote:
>> I understand that protein
>> parsimony can also be applied in PHYLIP, though I have never tried this.
>I believe the standard ("universal") codon translation protein
>parsimony (ProtPars) is used as default, with no option to do parsimony with
>equal weighting or protein parsimony based on other codes. One should
>still be able to use equal weighting if the data are not treated as
>protein data. Is this still correct, Joe?

PROTPARS is not able in version 3.5 to handle codes other than the
Universal code.  Our discrete-characters parsimony program does not allow
more than two states, and in that is much less general than PAUP.  So no,
you can't do "equal weighting" which I take to mean any amino acid can
change to any other.  You could fake it if there were 5 or fewer amino acids
by recoding them as nucleotides (plus Gap) and using DNAPARS but that seems
like cruel and unusual punishment.

Version 4.0 will allow multiple codes, and it will as well have far more
general discrete-characters parsimony programs but that is still far from
release, alas.

For "equal weighting" I'd use PAUP, or some other.

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

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