science software (mol biol/biochem/biology) under Linux

Ashok Aiyar aiyar at ebv.oncology.wisc.edu
Sat Oct 5 10:49:50 EST 1996

On 04 Oct 1996 16:41:22 -0600, zinc <zinc at zifi.genetics.utah.edu> wrote:
>i'm attempting to compile a list of software that either people have
>claimed runs under Linux or that is known to run under Linux for the
>people at Caldera (Caldera is Ray Noorda's ( of Novell fame ) new

There are several others ....

SignalScal - scan for transcription factor binding sites
           - version 4.07, written in C, compiles fine
           - ftp://biosci.umn.edu/pub/sigscan/unix

PIMA - pattern induced multiple sequence alignment
     - version 1.40, written in C, compiles fine
     - ftp://gc.bcm.tmc.edu/pub/software/pima

Predator - structural prediction based on multiple alignments
         - version 1.0, written in C, compiles fine
         - ftp://ftp.ebi.ac.uk/pub/software/unix/predator

ClustalW - pairwise and multiple alignments
         - version 1.60, written in C, compiles fine
         - ftp://ftp.ebi.ac.uk/pub/software/unix

Seqsee - protein sequence analysis package
       - version 1.2, written in C, compiles fine
       - available upon request from seqsee at procyon.biochem.ualberta.ca

Pratt - pattern discovery in sets of unaligned sequences
      - version 2.0, written in C, minor changes
      - ftp://ftp.ii.uib.no

Primer3 - PCR primer design
        - release 0.1, written in C, compiles fine
        - ftp://genome.wi.mit.edu

tacg - restriction analysis
     - version 1.5, written in C, compiles fine
     - ftp://mamba.bio.uci.edu/pub/tacg/

I'm sure you already have references for other common packages such
as Don Gilbert's sequence conversion utility - readseq, GDE, NCBI blast
etc. etc.

Ashok Aiyar, Ph.D.
Department of Oncology            email: aiyar at ebv.oncology.wisc.edu
University of Wisconsin-Madison                  tel: (608) 262-6697

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