JUCHMME: A Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis

Ioannis A. Tamposis, Konstantinos D. Tsirigos, Margarita C. Theodoropoulou, Panagiota I. Kontou, Georgios N. Tsaousis, Dimitra Sarantopoulou, Zoi I. Litou, Pantelis G. Bagos

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

JUCHMME is an open-source software package designed to fit arbitrary custom Hidden Markov Models (HMMs) with a discrete alphabet of symbols. We incorporate a large collection of standard algorithms for HMMs as well as a number of extensions and evaluate the software on various biological problems. Importantly, the JUCHMME toolkit includes several additional features that allow for easy building and evaluation of custom HMMs, which could be a useful resource for the research community. http://www.compgen.org/tools/juchmme, https://github.com/pbagos/juchmme. Supplementary data are available at Bioinformatics online.
Original languageEnglish
JournalBioinformatics
Volume35
Issue number24
Pages (from-to)5309–5312
ISSN1367-4811
DOIs
Publication statusPublished - 2020

Cite this

Tamposis, I. A., Tsirigos, K. D., Theodoropoulou, M. C., Kontou, P. I., Tsaousis, G. N., Sarantopoulou, D., Litou, Z. I., & Bagos, P. G. (2020). JUCHMME: A Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis. Bioinformatics, 35(24), 5309–5312. https://doi.org/10.1093/bioinformatics/btz533