[BiO BB] Re: Windows (XP) sequence analysis software
Ingrid.Marchal at univ-lille1.fr
Wed Dec 11 12:38:21 EST 2002
You can also try EMBOSS. It's an open source client-server package. It is
free and includes many valuable programs.
I think it is mainly intended for a text based usage but there are
graphical interfaces like jemboss, a java based interface.
At 18:01 11/12/2002, you wrote:
>Date: Tue, 10 Dec 2002 10:07:57 -0800
>From: Martin Gollery <mgollery at unr.edu>
>To: bio_bulletin_board at bioinformatics.org,
> "Julio.Harvey" <harvey at biology.ucsc.edu>
>Subject: Re: [BiO BB] Windows (XP) sequence analysis software
>Reply-To: bio_bulletin_board at bioinformatics.org
>I have used PHRAP, ClustalW, ClustalX, BLAST, Hmmer, seqweb, The Vector NTI
>suite, Jellyfish, DNAstar, DeCypher, and HMMpro on windows, as well as many
>others that I have probably forgotten.
>Quoting "Julio.Harvey" <harvey at biology.ucsc.edu>:
> > Hi,
> > Graduate student in evolutionary biology seeks software suggestions for
> > analyzing thesis data (nucleotide sequences) using Windows or (Red Hat)
> > Linux.
> > After years of using Macintosh based software to analyze my data, I am
> > frustrated in my search for PC based equivalents.
> > My needs and the Mac programs I have been using to satisfy them are as
> > follows:
> > 1) Assembly and editing of contigs from electropherogram data
> > (bi-directional sequencing of cloned genes) generated.
> > Currently use: AutoAssembler (Mac).
> > 2) Alignment of edited gene sequence data in preparation for entry
> > into PAUP.
> > Currently use: Sequence Navigator (Applied Biosystems) or ClustalX
> > (both Mac).
> > 3) Analysis of sequence similarity and subsequent production of gene
> > phylogenies using recent versions of PAUP (Swofford).
> > Currently using PAUP versions for Mac.
> > I would very much appreciate any advice leading to the acquisition of
> > Windows or even 'windows like' (ie Red Hat) based programs to accomplish
> > the above. I have heard of and (briefly) used the package "GCG" in the
> > past but do not currently have the means to purchase the same.
> > Do other such softwares exist or must I learn Unix or Linux to accomplish
> > my goals?
> > Many Sincere Thanks,
> > Julio Harvey
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