[BiO BB] Windows (XP) sequence analysis software

[Martin Gollery]

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
> 
> 
> 
> 
> 
> _______________________________________________________
> Julio Harvey
> Department of Ecology and Evolutionary Biology (EEB)
> A316 Earth and Marine Sciences
> University of California
> Santa Cruz, 95064
> (831) 459-2832 (lab)
> (831) 459-4882 (fax)
> "The way to do is to be".  -Lao-Tse
> _______________________________________________________
> 
> 
> 
> _______________________________________________
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> 


Martin Gollery
Associate Director of Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS200
(775)784-6048


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