:: DESCRIPTION
MRHMMs accommodates a variety of HMMs that can be flexibly applied to many biological studies and beyond.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2014 Feb 27. [Epub ahead of print]
MRHMMs: Multivariate Regression Hidden Markov Models and the variantS.
Lee Y1, Ghosh D, Hardison RC, Zhang Y.
:: DESCRIPTION
TileHMM is an R package designed for the analysis of ChIP-chip data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2008 Aug 18;9:343. doi: 10.1186/1471-2105-9-343.
Parameter estimation for robust HMM analysis of ChIP-chip data.
Humburg P1, Bulger D, Stone G.
:: DESCRIPTION
pHMM-Tree is the first software to generate a phylogeny of profile hidden markov models (HMMs).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Huo L, Zhang H, Huo X, Yang Y, Li X, Yin Y.
pHMM-tree: phylogeny of profile hidden Markov models.
Bioinformatics. 2017 Apr 1;33(7):1093-1095. doi: 10.1093/bioinformatics/btw779. PMID: 28062446; PMCID: PMC5860389.
:: DESCRIPTION
zipHMM is a library for hidden Markov models that exploits repetitions in strings to greatly speed up the calculations of the log likelihood of a sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.
Sand A, Kristiansen M, Pedersen CN, Mailund T.
BMC Bioinformatics. 2013 Nov 22;14:339. doi: 10.1186/1471-2105-14-339.
:: DESCRIPTION
Skylign is a tool for creating logos representing both sequence alignments and profile hidden Markov models.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models.
Wheeler, T.J., Clements, J., Finn, R.D.
BMC Bioinformatics Volume 15 (2014) p.7 DOI: 10.1186/1471-2105-15-7
:: DESCRIPTION
BSHMM is a software of methylation profile analysis using hidden Markov models.
::DEVELOPER
Laboratory of Computational and Quantitative Biology(LCQB)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MBPpred is a profile Hidden Markov Model based method capable of predicting membrane binding proteins (MBPs).
::DEVELOPER
The Biophysics and Bioinformatics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
MBPpred: Proteome-wide detection of membrane lipid-binding proteins using profile Hidden Markov Models.
Nastou KC, Tsaousis GN, Papandreou NC, Hamodrakas SJ.
Biochim Biophys Acta. 2016 Apr 2. pii: S1570-9639(16)30057-7. doi: 10.1016/j.bbapap.2016.03.015.
:: DESCRIPTION
mhsmm is a software of parameter estimation and prediction for hidden Markov and semi-Markov models for data with multiple observation sequences. The software is suitable for equidistant time series data, with multivariate and/or missing data.
::DEVELOPER
Jared O’Connell and Jonathan Marchini.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Jared O’Connell, Soren Hojsgaard (2011).
Hidden Semi Markov Models for Multiple Observation Sequences: The mhsmm Package for R.
Journal of Statistical Software, 39(4), 1-22.
:: DESCRIPTION
SATCHMO uses HMM-HMM scoring and alignment to simultaneously estimate a phylogenetic tree and a multiple sequence alignment (MSA).
SATCHMO-JS is a variant of the SATCHMO algorithm designed for scalability to large datasets. We use a jump-start (JS) protocol to reduce complexity, employing computationally efficient MSA methods for subgroups of closely related sequences and saving the computationally expensive HMM-HMM scoring and alignment to estimate the tree and MSA between more distantly related subgroups.
::DEVELOPER
the Berkeley Phylogenomics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Edgar, R., and Sjölander, K.,
SATCHMO: Sequence Alignment and Tree Construction using Hidden Markov models
Bioinformatics. 2003 Jul 22; 19(11):1404-11.
Hagopian, R., Davidson, J., Datta, R., Samad, B., Jarvis, G., and Sjölander, K.
“SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction”,
Nucl. Acids Res. (2010) 38(suppl 2): W29-W34., doi:10.1093/nar/gkq298