PROGRAM OPTIMIZE
Andrew Abbott
Biological Software Currently
Available
I am in the process of testing these, and so cannot give final advice
on them. Where I know them I give addresses, computer info, etc. Most important
biological sequencing programs are now shareware, in contrast to the situation
until quite recently.
ATBE
approximate tree matching, Wang, Jeong, Zhang, Shasha NYU dept computer
science Vingron/Argos alignment of distant relations, Multiple alignment
VINGRON@embl.bitnet
SOMAP Parry-Smith and Attwood, CABIOS 7:233-35. multiple alignment VAX VMS,
interactive symbolic manipulation program (like Explore) Astbury Dept of
Biophysics and Genetics, Univ of Leeds, England ADSP Parry-Smith and Attwood, CABIOS 8:451-459 front end for SOMAP, mostly
of biological use MASH Chappey et al. CABIOS 7:195-202 - multiple alignment in PASCAL for
DOS or MAC. MUSEQUAL Berger and Munson CABIOS 7:473-481 iterative mult alignment PC based
with environment. MACAW Schuler, Altshcul, Lipman, Proteins 9:180-190 multiple alignment, up
to 16 seqs, Windows 3.0 National Center for Biotechnol Information ncbi.nlm.nih.gov
FASTA
Pearson and Lipman, PNAS 85:2444-8. database search for sequences, William
Pearson, wrp@virginia.bitnet
MSA Lipman, Altschul, Kececioglu PMAS 86:4412-4415. multiple alignment,
(MCBI?) Alexandrov Alexandrov CABIOS 8:339-345 local multiple alignment. MATCHBOX
Depiereux and Feytmans CABIOS 8:501-509 multiple alignment, up to 200
sequences, 100,000 elements (!) EDEPIEREUX@bnandp51.bitnet
SERPENT Various authors CABIOS 8:295-296 This is the SPSS of sequence programs,
but designed for biological inputs VMS, Unix, soon to be commercial CLUSTAL V Higgins, Bleasby, and Fuchs - Multiple Sequence Alignment in C. EMBL
file server (Netserv@embl.Heidelberg.de) Boguski, Hardison, Schwartz, Miller Multiple alignment toolkit C for Unix, but translatable. groucho.cs.psu.edu
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Preliminary Notes
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