PCMA - Profile Consitency Multiple sequence Alignment


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Please send bug reports, comments etc. to one of:
	jpei@mednet.swmed.edu
	grishin@chop.swmed.edu

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                  POLICY ON DISTRIBUTION OF PCMA

PCMA has used codes from  Clustal W, version 1.81.  Clustal W, 
developed by Thompson JD , Higgins DG and Gibson TJ, is freely available to the
user community.  Commercial distributors of Clustal W must take out a 
NON-EXCLUSIVE LICENCE from the authors of Clustal W (gibson@embl-heidelberg.de, 
thompson@embl-heidelberg.de or d.higgins@ucc.ie).  According to this policy, 
PCMA is free for non-commercial uses.  Commercial uses is disallowed. 

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                       Version 2.0


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                 Installation instruction

In the directory of src, execute the following two commands

make clean

make



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				References

Pei, J., Sadreyev, R., Grishin, N.V., (2003) PCMA: a program for fast
and accurate multiple sequence alignment, Bioinformatics.19(3):427-428.

Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the
sensitivity of progressive multiple sequence alignment through sequence
weighting, positions-specific gap penalties and weight matrix choice.  Nucleic
Acids Research, 22:4673-4680.

Notredame, C., Higgins, D.G., and Heringa, J. (2000). T-Coffee: A novel method 
for fast and accurate multiple sequence alignment, J Mol Biol 302, 205-17.