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Phylogenetic compatative programs-shareware?

Warren Lathe madda at troi.cc.rochester.edu
Thu Aug 31 10:37:13 EST 1995


In <glarson-300895093822 at 151.112.27.59> glarson at ccmail.llu.edu (Garry P. Larson) writes:

>I am interested in comparing certain gene regions (coding and noncoding)
>between closely related viral variants.  Being new to the game, does anyone
>know if there is (are) a USER FRIENDLY (of course this is relative),
>Mac-based  programs available via ftp transfer, etc. or the Web to
>accomplish this task.  My goal is to compare an unknown sequence to a known
>database which will enable me to place the unknown into a specific subgroup
>in the database.  I would anticipate that these sequences are 90-95%
>homologous in the region being examined.

>Many thanks,

>GLarson


You can get PAUP from (http://www.genethon.fr/exterieur/bio_catal.html#PAUP) 
Phylip from (ftp://evolution.genetics.washington.edu/pub/) and other programs
from (gopher://megasun.BCH.UMontreal.CA:70/11/CMB/Phylogeny)

These are all pretty good and relatively simple to use and learn. You might
try out Pedro's Biomolecular tools (http://www.public.iastate.edu/~pedro/research_tools.html)  This has a large listing of online resourses that would
compare sequences to databases (Blast search), bibliographies, software, etc.

Trey

_________________________________________
Warren C. Lathe III (Trey)
Biology Department
University of Rochester
email:  trey at thelab.biology.rochester.edu
_________________________________________
-- 
The juvenile seasquirt wanders through the sea searching for a suitable rock
or coral to cling to and make its home for life. For this task it has a
rudimentary nervous system. When it finds its spot and takes root, it
doesn't need its brain anymore so it eats it.It's rather like getting tenure.



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