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Genetical software for Linux

Jonathan Epstein epstein at gold.nlm.nih.gov
Thu May 18 13:38:50 EST 1995


Seyeon Weon (sywon at bioneer.kaist.ac.kr) wrote:
> Peter Van Osta (pvanosta at allserv.rug.ac.be) wrote:
> : Hello,


> : I am looking for Software running on Linux for sequence analysis (editing, 
> : alignment, ...) and manipulation .I am also desperately looking for the 
> : auxiliary software for Linkage analysis (lcp, ...) that can be compiled with 
> : gcc under Linux.

> : Linux compatible software for Database searching (GDB, Genbank) running under 
> : XFree ?

> : (I am interested in general in software for (human) genetical research running 
> : under Linux and/or XFree)

> 	We are setting up a Pentium Linux server for biologists, too.
> (With 64MB RAM, 6GB hard disk, and more than hundred user accounts,
> we may call it a server...)  Here is the list of molecular biology
> related softwares we've succeeded with gcc and Linux.

> clustalw v1.5
> fasta v2.0x
> xylem v1.5
> treealign v1.0
> fsap 6-OCT-94
> msu v1.4
> mailfasta v3.2
> Huang's programs (cap, lcp, gap, map)
> msa v2.0
> naview v1.0
> pratt 16-MAR-95
> primer-mit v0.5
> readseq 30Dec92
> dbget v1.2
> sigseq v1.0
> signal
> seqalign
> phylip 3.5c
> statalign
> GDE
> Rasmol

> 	As you can see, we haven't succeeded with blast yet.  Has anyone?
> We may need an ftp server for archiving Linux binaries and a mailing
> list.

> --
> ==================================================================
>   Seyeon Weon            E-MAIL : sywon at bioneer.kaist.ac.kr
>   Dept. of Biological Sciences
>   Korea Advanced Inst. of Sci. and Tech. ( KAIST )


Don't forget about Network Entrez ... this works too, although I haven't
built it in a while (since I lack a suitable host).

The NCBI toolbox, which includes full source code for Network Entrez, is at
ftp://ncbi.nlm.nih.gov/toolbox/ncbi_tools/ncbi.tar.Z.

CD-ROM Entrez should work too, although I haven't tried it.

Cheers,

- Jonathan


Jonathan Epstein                                epstein at ncbi.nlm.nih.gov
National Center for Biotechnology Information   Phone: (301)496-2475
National Library of Medicine                    Building 38A, Room 8N805
National Institutes of Health                   8600 Rockville Pike
                                                Bethesda, MD 20894





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