Need program to calculate sequence similarities

Tim Hutchin hutchin at hsc.usc.edu
Wed Jan 18 08:04:20 EST 1995


In article <3fjlq3$cj7 at gaia.ucs.orst.edu>, gordond at ava.bcc.orst.edu
(Douglas Gordon) wrote:

>         I am interested in finding a program that will calculate 
> similarities among a fairly large (20 - 25) group of aligned DNA 
> sequences.  I have access to several different UNIX platforms as well as 
> PCs and MACs.  Ideally the program should accept the files in a standard 
> format (ie. GCG or Genbank) and give distances as well.  It would also be 
> nice if the output was close to publication quality.  Thanks in advance 
> for any help you can give me.


The PHYLIP package from Joe Felsenstein has a whole bunch of programs.  It
includes several for calculating distances (I have been able to do several
hundred!), and accepts them in most formats.  Versions are available for
UNIX and MACs, by FTP - email me if you want any further details.



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