[Bioperl-l] Bio::Tools::Run::PiseApplication : parameters changes in seqgen

Catherine Letondal letondal at pasteur.fr
Wed Aug 3 09:00:30 EDT 2005


The Pise/bioperl interface of the seq-gen program 
(http://bioweb.pasteur.fr/seqanal/interfaces/seqgen-simple.html) has 
changed. We have added new parameters, modified one and changed some 
parameters' type from Integer to Float:

Changes in parameters:
         - added options invar_site (-i), random_seed (-z), write-ancest 
(-wa),   write-sites (-wr), partition_numb (-p)
         - fixed bug in Phylip option: it was -p now it's a vlist: -op, 
-or, -on
         - changed type of some options type from integer to float 
(scale_branch, scale_tree, rate123, shape, freqACGT, transratio)

Please tell us if there is any trouble.


Catherine Letondal -- Institut Pasteur

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