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MACAW -> phylogeny

Michael A. Lonetto lonetto at CGL.UCSF.EDU
Fri Mar 10 17:56:00 EST 1995

Does anyone have a quick means of converting the text output of MACAW
alignments into some format that SeqApp, GCG, ReadSeq, or some
other general purpose program can read?  I can generate something like
a Phylip interleaved format pretty quickly with a text editor, but this 
is a dead end since the file isn't read by any of my conversion programs
(they all think it's a sequential file).  I can hack at it a bit more, in
case I left some blanks that shouldn't be there, but there has to be a 
better way.  

The ideal solution would be something simple that converts it to either
GCG/msf, Pearson/Fasta or Intelligenetics format, preserving the alignment 
(why doesn't  Macaw write Pearson format?  It can read it.)  From there manual
editting and conversion to Phylip or Nexus is easy.  

If nothing exists I have a C-program I wrote a while back to convert sequential
to interleaved that I could hack to work backwards, but it seems like an ideal 
problem for some perl hotshot ;-)

Michael Lonetto // Phone:  415-476-1493 // Email: lonetto at cgl.ucsf.edu 
U$nailMail: UCSF Division of Oral Biology,  San Francisco, CA 94143-0512

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