intent to package: dstool, hmmer
Anyone else started these, or have info ?
gene sequence analysis tool
o About this software...
HMMER is an implementation of profile HMM methods for
sensitive database searches using multiple sequence alignments as
Basically, you give HMMER a multiple sequence alignment as input;
it builds a statistical model called a "hidden Markov model"
which you can then use as a query into a sequence database
to find (and/or align) additional homologues of the sequence family.
o Getting HMMER
WWW home: http://hmmer.wustl.edu/
The DsTool program is the property of:
Center of Applied Mathematics
Ithaca, NY 14853
and may be used, modified and distributed freely, subject to the following
Any product which incorporates source code from the DsTool
program or utilities, in whole or in part, is distributed
with a copy of that source code, including this notice. You
must give the recipients all the rights that you have with
respect to the use of this software. Modifications of the
software must carry prominent notices stating who changed
the files and the date of any change.
DsTool is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of FITNESS FOR A PARTICULAR
PURPOSE. The software is provided as is without any obligation on the part
of Cornell faculty, staff or students to assist in its use, correction,
modification or enhancement.
I. DsTool Program Description
There is a critical need for computational environments that provide
effective tools for exploring dynamical systems with minimal effort on the
part of the user. Research that relies upon the investigation of
dynamical systems would be greatly enhanced by a standard, uniform
environment for the exploration of these systems with computers.
The explosion of the graphical computational capabilities of relatively
in- expensive desktop computers in the past few years makes the
development of such an environment both feasible and timely. The program
described here, called DsTool (pronounced dee-ess-TOOL), describes an
implementation of one such environment for the Sun UNIX workstation. It
is an efficient research tool that integrates a friendly graphical user
interface, data management capabilities, a rich set of numerical
algorithms together with the flexibility to add more algorithms and
communicate data with other programs. DsTool has been implemented for use
with the X Window system from MIT and is based upon the program kaos,
written by S. Kim and J. Guckenheimer.
An experimental release that uses Tcl/Tk for its user interface has been
placed in the subdirectory Version_tk.
John Lapeyre <email@example.com>