Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
How to integrate GeneMark.hmm results into Artemis? Caro241 Bioinformatics 1 11-06-2012 09:56 AM
BMC Bioinformatics: PileLine toolbox to handle genome-position files in NGS studies. gonvader Literature Watch 2 02-10-2011 04:54 AM
2 Bioinformaticians wanted Inti Academic/Non-Profit Jobs 0 02-04-2009 06:29 AM
An HMM approach to genome-wide identification of differential histone modification si jlli Bioinformatics 0 08-06-2008 06:54 AM

Thread Tools
Old 08-05-2012, 11:05 AM   #1
Junior Member
Location: Switzerland

Join Date: Jan 2009
Posts: 9
Default HMM library/toolbox wanted

I am planning to extend my existing software by using HMMs in some modeling step. Therefore I looked for some existing libs. I have found GHMM ( and HTK (, but haven't tested them yet.

Did anyone try using these, or possibly some other libraries? Are they easy to use and comprehensive? My existing software is in C++, so it would be best to use C/C++ libs. But if there is an outstanding Python/Perl/Matlab/R toolbox I can turn my eye on it.

merilius is offline   Reply With Quote
Old 08-05-2012, 03:38 PM   #2
Location: Cambridge, MA

Join Date: Apr 2011
Posts: 18

It depends what you want to do. I've looked at HMMlib ( as well as GHMM but didn't seriously use either.

If all you need is something that will take a transition matrix and vector of emission probabilities, then any of them should be fine. I've never found a library that attempts to handle anything more complicated like sparse or time-dependent transition matrices or custom array/matrix classes, and have had to write my own library for things like that.
alec is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 06:57 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO