Overview

HMMEditor is a visual editor for profile Hidden Markov Model (pHMM). With HMMEditor you can

• Visualize a pHMM
• Edit a pHMM
• Show Viterbi path of a sequence

PHMM is used by Hmmer, Pfam. HMMEditor is published under GNU License.

Start from 1.1, HMMEditor support Pfam database. Download and unzip the Pfam archive, you can access individual pHMM inside Pfam database from HMMEditor directly.

Launching HMMEditor 1.1 using Java Web Start

Here are some test hmm and sequence files you can use for you test.

Document

HMMEditor manual

Citing HMMEditor

J. Dai and J. Cheng. HMMEditor: A Visual Editing Tool for Profile Hidden Markov Model. BMC Genomics. 9(S1):S8, 2008.

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