[BiO BB] Re: Windows (XP) sequence analysis software

[Ingrid Marchal]

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.

http://www.hgmp.mrc.ac.uk/Software/EMBOSS/

cheers,
Ingrid

At 18:01 11/12/2002, you wrote:
>Message: 1
>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.
>Marty
>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