Tag: Model

HHMMiR 1.2 – Prediction of microRNAs using Hierarchical Hidden Markov models

HHMMiR 1.2

:: DESCRIPTION

HHMMiR is a novel approach for de novo miRNA hairpin prediction in the absence of evolutionary conservation. HHMMiR implements a Hierarchical Hidden Markov Model (HHMM) that utilizes region-based structural as well as sequence information of miRNA precursors.

:: DEVELOPER

Benos Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 HHMMiR

:: MORE INFORMATION

Citation:

S. Kadri, V. Hinman, P.V. Benos,
“HHMMiR: Efficient de novo Prediction of MicroRNAs using Hierarchical Hidden Markov Models“,
BMC Bioinformatics (Proc APBC 2009) (2009) 10 (Suppl 1):S35.

MBCluster.Seq 1.0 – Model-Based Clustering for RNA-seq Data

MBCluster.Seq 1.0

:: DESCRIPTION

MBCluster.Seq : Cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other digital gene expression (DGE) data

::DEVELOPER

Yaqing Si <siyaqing at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 MBCluster.Seq

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 15;30(2):197-205. doi: 10.1093/bioinformatics/btt632. Epub 2013 Nov 4.
Model-based clustering for RNA-seq data.
Si Y1, Liu P, Li P, Brutnell TP.

Clumpak 20150326 – Model-based Population Structure Analysis

Clumpak 20150326

:: DESCRIPTION

Clumpak (Cluster Markov Packager Across K) is a method that automates the postprocessing of results of model-based population structure analyses.

::DEVELOPER

Mayrose Lab, Tel Aviv University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX
  • Perl

:: DOWNLOAD

 Clumpak

:: MORE INFORMATION

Citation:

Mol Ecol Resour. 2015 Feb 12. doi: 10.1111/1755-0998.12387.
Clumpak: a program for identifying clustering modes and packaging population structure inferences across K.
Kopelman NM1, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I.

RNAenn – Energy Parameters and novel algorithms for Extended nearest Neighbor Energy Model of RNA

RNAenn

:: DESCRIPTION

RNAenn computes the partition function and minimum free energy secondary structure for RNA with respect to an extended nearest neighbor energy model.

::DEVELOPER

Clote Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAenn

:: MORE INFORMATION

Citation

Energy parameters and novel algorithms for an extended nearest neighbor energy model of RNA.
Dotu I, Mechery V, Clote P.
PLoS One. 2014 Feb 21;9(2):e85412. doi: 10.1371/journal.pone.0085412.

phyloExpCM 0.32 – Phylogenetic Analysis with experimentally determined Codon Models

phyloExpCM 0.32

:: DESCRIPTION

phyloExpCM is a Python package to implement experimentally determined codom models of substitution for phylogenetics.

::DEVELOPER

Bloom Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 phyloExpCM

:: MORE INFORMATION

Citation

Bloom JD.
An experimentally determined evolutionary model dramatically improves phylogenetic fit.
Mol Biol Evol. 2014;31:1956-1978.

SoloDel 1.0.0 – Somatic Low-frequent Deletion Caller Model

SoloDel 1.0.0

:: DESCRIPTION

SoloDel is a Java based somatic deletion caller designed for whole-genome sequencing data from unmatched samples. SoloDel is specialized for identifying somatic deletions with frequently existing sampling issues : low mutational frequency in cell population and absence of the matched control samples.

::DEVELOPER

SoloDel team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 SoloDel

:: MORE INFORMATION

Citation

SoloDel: A probabilistic model for detecting low-frequent somatic deletions from unmatched sequencing data.
Kim J, Kim S, Nam H, Kim S, Lee D.
Bioinformatics. 2015 Jun 11. pii: btv358.

MACE 1.2 – Model-based Analysis of ChiP-exo

MACE 1.2

:: DESCRIPTION

MACE is a novel analysis framework to detect two binding borders of protein-DNA interactions from ChIP-exo data.

::DEVELOPER

Wei Li’s Computational Epigenomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 MACE

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Nov 10;42(20):e156. doi: 10.1093/nar/gku846. Epub 2014 Sep 23.
MACE: model based analysis of ChIP-exo.
Wang L, Chen J, Wang C, Uusküla-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, Li W

nondetects 2.16.0 – Model and Impute non-detects in qPCR data

nondetects 2.16.0

:: DESCRIPTION

nondetects is a suit of methods to model and impute non-detects in the results of qPCR experiments.

::DEVELOPER

Matthew N. McCall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bioconductor

:: DOWNLOAD

 nondetects

:: MORE INFORMATION

Citation

On non-detects in qPCR data.
McCall MN, McMurray HR, Land H, Almudevar A.
Bioinformatics. 2014 Apr 23. pii: btu239

PeptideBuilder 1.0.4 – Python Library to Generate Model Peptides

PeptideBuilder 1.0.4

:: DESCRIPTION

PeptideBuilder is a simple Python library to construct models of polypeptides from scratch.

::DEVELOPER

Claus Wilke’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 PeptideBuilder

:: MORE INFORMATION

Citation

Tien MZ, Sydykova DK, Meyer AG, Wilke CO. (2013)
PeptideBuilder: A simple Python library to generate model peptides.
PeerJ 1:e80

GPSeq 0.5 – Using the Generalized Poisson distribution to model sequence read counts from high throughput sequencing experiments

GPSeq 0.5

:: DESCRIPTION

GPSeq is a software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons.

:: DEVELOPER

Liang Chen’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • R package/Perl/C Compiler

:: DOWNLOAD

 GPSeq

:: MORE INFORMATION

Citation:

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data.
Srivastava S, Chen L.
Nucleic Acids Res. 2010 Sep;38(17):e170. doi: 10.1093/nar/gkq670.