Fitch parsimony how to ?

[Jean-Michel Richer]

Hi,

  how can I proceed to use POY with Fitch parsimony criterion ?

When I do the following:

load("tst01.fasta")

build(10)

POY reports :

Storing 10 trees with costs 412. to 438.

However, under Fitch parsimony the best score is 545 !!

This means that by default POY is not using Fitch criterion

So how do I tell poy to use Fitch ?

Note: my input file (tst01.fasta) as the following format

>N0001

??AA?CAC??C?ACCC?ACA?ACACCACAAAACACAAAAACAACA?CCCAACAACA??C?A

>N0002

CCC?C??AACACAAA?CCAA?AAA?C?CAAAA?A?A??A?AACACCCCACCCCAC?CACCC

>N0003

....

[Ward Wheeler]

Hello,

You are entering unaligned sequences.  You need to enter with hennig86 or Nexus format and specify the characters as non-additive to use Fitch optimization.

W

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[Nicholas Lucaroni]

By default, fasta files are read as unaligned sequence data, stripping out any previous alignment information. You'll have to specify that the files are prealigned by the following argument to the command,

  read( prealigned:("FILENAME", tcm:(1,1)) )

- Nicholas Lucaroni