multiple alignment

James McInerney jamm at nhm.ac.uk
Wed Jun 11 10:07:28 EST 1997


Berke, Tamas wrote:
> 
> Dear Colleagues:
> Could any of you name a program (PC or UNIX) which can help me to align
> corresponding nucleic acid sequences to the already aligned (Clustal)
> amino acid sequences?
> Your assistance is appreciated.
> Tamas Berke

I have coded a little program that should compile on most unix machines
for introducing gaps into DNA sequences according to where they appear
in an amino acid alignment.  It is available as C source code or
compiled for the PowerPC at:

ftp://ftp.nhm.ac.uk/pub/gcua/Putgaps

Its neither elegant nor fancy (none of my code is!) and I cannot provide
any guarantees, but...

Bill Pearson also distributes a program called mrtrans (I think) which
also does this.  It is available from:

ftp://ftp.virginia.edu/  (I hope that's correct).

regards,

James.

p.s. read the documentation with putgaps!!!
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James O. McInerney               email: J.mcinerney at nhm.ac.uk
Senior Scientific Officer,       phone: +44 171 938 9247
Department of Zoology,           Fax:   +44 171 938 9158
The Natural History Museum,
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