Software to help searching Mol. databases

[Steve Thompson]

In Article <Pine.A41.3.94.961016213334.133068J-100000 at acs3.acs.ucalgary.ca>,
"B.McVittie" <bjmcvitt at acs.ucalgary.ca> wrote (in part):

>I am currently investigating the phylogenetic position of tarsius within
>primates. I consider myself  to be 'competent' regarding  theoretical
>issues in molecular phylogeny, but my practical 'know-how' is
>non-existent.
>I would like to search the big databases (genbank,embl, etc.) for all
>tarsier sequences which have recorded orthologies in other primate
>species. However I have no idea how to go about this.
>Specifically:   -How can I search for sequences by species? 
>                -Is it possible to use sequences from one species to
>                 search for orthologous sequences in other spp?
>                -What types of software can be used towards this end?
>
>Brad McVittie bjmcvitt at acs.ucalgary.ca.  

This is exactly the type of stuff that NCBI's NetEntrez software excells at!
Get it at www.ncbi.nlm.nih.gov; install it; learn it; use it.  It is great.

>                -What software works well for storing sequence data?
>                -What software is good for multi-spp alignments? How
>                 compatible is such software with analytic programs
>                 (Paup,Phylip,etc.) with regard to integrating gap
>                 penalties into analyses.

This is a much more difficult decision; either do it all on your own with
"free" stuff off the web, etc; or use a large comprehensive software package
on a server, e.g. GCG; or use some local, desktop product, e.g. GeneWorks. 
They're all only as good as you learn how to operate them and they will all
take some learning.  All biocomputing software, it seems, has their own
particular format requirements - get Don Gilbert's ReadSeq to cope with most
of them.  Good luck with the learning or else hire it out.

                                            - Steve

                                Steven M. Thompson
              Consultant in Molecular Genetics and Sequence Analysis
        Visualization, Analysis & Design in the Molecular Sciences (VADMS)
             Washington State University, Pullman, WA 99164-4660, USA
                  AT&Tnet:  (509) 335-3179  FAX:  (509) 335-9688
                    INTERnet:  thompson at ribozyme.vadms.wsu.edu