JMILLER%VXBIO.SPAN@STAR.STANFORD.EDU (08/19/90)
To answer Jay Zuccola's request; Multiple sequence alignment on the mac is a big problem, since none of the programmers who write these programs write for the mac. Thus, any program will be a port, and I am apparently the only person who has done this. I ported THREE from Russell Doolittle's lab in 1987. It has obvious problems when the sequences don't start at about the same place. More recently, I produced a mac version of CLUSTAL, which can align both DNA and protein sequences. It required a MacII and 3megs memory for reasonable performance. Unfortunately, IntelliGenetics owns the rights to this program, so I can't distribute it. I sent the source code for the port to Chris Dow last spring, so mabye all or part of CLUSTAL will appear in the Mac sequence analysis program they have developed. I also have gotten Russell Doolittle's package to 'run' on the mac. This package includes programs like PRELAIGN,TREE,SCORE, etc. It does a good job of alignment. Unfortunately, there are some subtle compiler differences between MPW C and the unix compiler used for the programs, which has introduced bugs I haven't been able to fix. The programs demand >4 megs RAM, even though they should run in about 2.5 megs, and have random,sequence-dependent crashes. I have sent the source to a programmer friend of mine, Carl Lawyer, to see if HE can figure out the problem. If and when these programs are fixed, they will be avaialble for free. That's all I know. Since so many people have macs these days, it would be nice to have a program of this type. I don't have the time to write one from scratch. If anyone out there is interested in either (1)writing a multiple sequence alignment program for the mac, or (2)porting their software to the mac, they are welcome to contact me about the whys and wherefores. -Peter Markiewicz