UNIX Parsimony Programs

Dave Carmean carmean at sfu.ca
Fri Nov 3 21:38:55 EST 1995

SeqApp does a very good job of converting most format to other formats. 
You may have to simplify the header and remove any formatting after the
data.  Give SeqApp additional memory to handle that many taxa.  MacClade
will also create PHYLIP files from Nexus formatted files.

A third possibility is to open your Nexus sequential file in Word (5.1)
(using a non-proportional font such as courier), then after the first
block of data with the names, delete the whole column (block) of names
using the option key and scrolling down with the mouse.  This will give
you the PHYLIP sequential format.  However, I do not like this format, as
it is difficult to delete, add, or rearrange taxa.

Dave Carmean
carmean at sfu.ca 

 In article <v01510100acbac1380e9d@[]>, amcarthu at UVic.CA
(Andrew G. McArthur) wrote:

> Colleagues,
> I have a large (98 taxa, 200 bp) NEXUS file that I have tried to analyse
> with PAUP.  Needless to say, it is slow.  I have PHYLIP for UNIX on a new
> SPARC station and wish to try it that way - does anyone have a conversion
> utility for converting NEXUS files to PHYLIP infiles?  Also, what other
> parsimony programs are available for UNIX systems?  I know a UNIX version
> of PAUP is forthcoming, but is there anything else I could try in the
> meantime.  Much thanks!
> Andrew

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