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@sprsgi.med.harvard.edu * * Center for Blood Research phone: 617-278-3200 * * 200 Longwood Ave. Room 251 fax: 617-278-3232 * * Boston MA 02115 * *******************************************************************************