sequence identity: have answer

["Timothy A. Springer Ph.D." <springer AT sprsgi.med.harvard.edu>]

This is not hard to do.  One just has to specify a sequence identity matrix
and then convert it in a spreadsheet to the complement.  Only distance
matrices can be used to make the matrix.  The following error message was
helpful to me:

seqcomp_W> RR_FILE must be a distance matrix;
  automatically converted: new_elem = -old_elem + max_elem


 >It would be very nice to have sequence identities and other parameters
that are placed in tables
>above or below a diagonal in the log file also be capable of being written
>in a square matrix format
>like they are for the .mat files that you offer for PHYLIP inputs.  I
>often want to calculate
>averages, or make dendrograms for parameters that are not output to mat
>files.  It takes a
>lot of time to reformat so for example i can get a calculation by excel.
>I do not have any
>other good way to calculate % identity for a lot of sequences.


*******************************************************************************
*  Timothy A. Springer, Ph.D.                                                 *
*  Latham Family Professor of Pathology                                       *
*  Harvard Medical School            e-mail: springer AT sprsgi.med.harvard.edu  *
*  Center for Blood Research            phone:  617-278-3200                  *
*  200 Longwood Ave.  Room 251          fax:    617-278-3232                  *
*  Boston MA 02115                                                            *
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