[BiO BB] Windows (XP) sequence analysis software

[Julio.Harvey]

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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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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