mhsmm 0.4.16 – Parameter Estimation and Prediction for Hidden Markov and semi-Markov models for data with multiple Observation Sequences

mhsmm 0.4.16

:: 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

  • Linux/Windows/MacOsX
  • R package

:: DOWNLOAD

  mhsmm

:: 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.

MBPpred – Prediction of Membrane lipid-Binding Proteins using profile Hidden Markov Models

MBPpred

:: 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

  • Web browser

:: 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.

Skylign – Creating Logos Representing both Sequence Alignments and profile hidden Markov models

Skylign

:: DESCRIPTION

Skylign is a tool for creating logos representing both sequence alignments and profile hidden Markov models.

::DEVELOPER

Skylign team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Skylign

:: 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

zipHMM 1.0.1 – Library for very fast Likelihood Computations for Hidden Markov Models

zipHMM 1.0.1

:: 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

Thomas Mailund

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 zipHMM

:: 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.

BSHMM – DNA Methylation Analysis, based on hidden Markov models

BSHMM

:: 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

  • Linux

:: DOWNLOAD

 BSHMM

:: MORE INFORMATION

TileHMM 1.0-6 – Hidden Markov Models for ChIP-on-Chip Analysis

TileHMM 1.0-6

:: DESCRIPTION

TileHMM is an R package designed for the analysis of ChIP-chip data.

::DEVELOPER

CSIRO Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

 TileHMM

:: 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.

MRHMMs 2 – Multivariate Regression Hidden Markov Models and the variantS

MRHMMs 2

:: DESCRIPTION

MRHMMs accommodates a variety of HMMs that can be flexibly applied to many biological studies and beyond.

::DEVELOPER

MRHMMs team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/ WIndows
  • C Compiler

:: DOWNLOAD

 MRHMMs

:: 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.

HMMoC 1.3 – Compiler for Hidden Markov Models

HMMoC 1.3

:: DESCRIPTION

HMMoC translates a high-level description of a hidden Markov model into efficient C++ code

::DEVELOPER

Comparative Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Java
  • C++ Compiler

:: DOWNLOAD

 HMMoC

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Sep 15;23(18):2485-7. Epub 2007 Jul 10.
HMMoC–a compiler for hidden Markov models.
Lunter G.

SATCHMO 2.06 / SATCHMO-JS – Simultaneous Alignment and Tree Construction using Hidden Markov Models

SATCHMO 2.06 / SATCHMO-JS

:: 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

  • Linux
  • C++ Compiler
  • Python
  • BioPython

:: DOWNLOAD

  SATCHMO / SATCHMO-JS

:: 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