debry@ds1.scri.fsu.edu (Ron DeBry) (02/07/91)
If anyone is interested in running Joe Felsenstein's DNA maximum likelihood phylogeny program (dnaml) on a Cray under UNICOS, I have a version which is much faster (on a Cray, that is) than the distribution version. I replaced the innermost loops of two of the most frequently called subroutines with vectorizable FORTRAN modules, which are linked to the rest of the program with segldr. It works here on a YMP 4/432 - I guess that it should also work as is on an XMP - I have no idea whether it will work properly on a Cray-2. As a rough benchmark, I ran a 15 species, 2000 bp data set, with global branch swapping, in less than 15 minutes of cpu time. Your mileage will vary, depending on the number of patterns and numerous other parameters. I have also added an option which I needed badly - E for Eliminate taxa. This allows you to keep the same input file with all the species, but only analyze a subset. I have tested this fairly rigorously so far, and am continuing to try & dream up ways to make it crash before I let anyone else try it. I intend to also modify the dnamlk program (maximum likelihood with an assumed molecular clock), although I haven't actually done it yet. If someone asks for it, I'll be more likely to finish that quickly, since I don't have a need to run that program right now myself. I do not intend to modify the restriction site maximum likelihood program, for two reasons. First, the innermost loops in that program are very small (the number of iterations equals the length of the recognition sequence), so there would only be a small gain in speed, or even a loss in some cases. Second, restriction site data sets are likely to be much smaller than sequence data sets. I have a nine species, 140 site data set that runs in less than a minute of cpu time with the unmodified program. If you have a really massive restriction site data set, let me know, and we can discuss what might be done. If you want the modified dnaml program, contact me at one of the following addresses (ds1 is preferred): InterNet: debry@ds1.scri.fsu.edu or debry@fsu.scri.fsu.edu BitNet: DEBRY@FSU Mail: Ron DeBry Department of Chemistry Florida State University Tallahassee, FL 32301 Phone: (904) 644-4233