Software to help searching Mol. databases

[B.McVittie]

Hello ALL:

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?
		-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.
>From these questions you can see how uneducated i am on these issues.
Any info, or refs. to literature discussing these topics would be GREATLY
appreciated. 
Thanks in advance,
Brad

P.S. you can e-mail me directly at bjmcvitt at acs.ucalgary.ca.  

Brad McVittie
Dept. of Anthropology
University of Calgary
Calgary, Alberta, Canada
T2N 1N4
Office ph:(403) 220- 2848
Dept.Fax: (403) 284- 5467