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.

Tim Springer