Hmmer

Category(ies): Bioinformatics

Version: v2.3.2, v1.8

Author / Distributor:
Sean Eddy
Dept. of Genetics, Washington University School of Medicine

Hidden Markov models (HMMs) are statistical models of the primary structure consensus of a sequence family. Bayesian probability theory is applied to guide how all the probability (scoring) parameters should be set.

altix: running program | Documentation | Installation | System

Running Program:

e.x.

hmmalign [-options] <hmm file> <sequence file>

hmmbuild, hmmcalibrate, hmmconvert, hmmmit, hmmfetch, hmmindex, hmmpfam, hmmsearch

Documentation:

Available at here

Installation:

Application and license aquired from http://hmmer.janelia.org

System(s): Unix

inQuiry: not available at inQuiry

pcluster: Not available on pcluster

rcluster,IOB: running program | Documentation | Installation | System

Running Program: also refer to submit jobs to queues at rcluster,IOB

Version 2.3.2 is at /usr/local/hmmer/hmmer-2.3.2
Version 1.8 is at /usr/local/hmmer/hmmer-1.8
/usr/local/hmmerlatest is linked to Version 2.3.2
/usr/local/hmmerlatest is in the systemwide path

e.x.

bsub -q queueName hmmalign [-options] <hmm file> <sequence file

Documentation:, available at rcluster man command, and here is the Hmmer User Guide in pdf format.

Installation: Source code and license aquired from http://hmmer.janelia.org
gcc compiler with multithread enabled. HMMER_NCPU set to 2 in /etc/profile.d/hmmer.sh

System(s): Unix