TagMix – Genome-wide Tag SNPs Selection

TagMix

:: DESCRIPTION

TagMix is an integrated cross-populations LD-based, haplotype-based and principal component analysis genome-wide tag SNPs selection algorithm to efficiently identify informative variants, prioritized across multi-populations of low LD and high diversity populations for custom chip array.

::DEVELOPER

Emile CHIMUSA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TagMix

:: MORE INFORMATION

mRMRe 2.0.9 – Parallelized mRMR Ensemble Feature Selection

mRMRe 2.0.9

:: DESCRIPTION

mRMRe contains a set of function to compute mutual information matrices from continuous, categorical and survival variables. It also contains function to perform feature selection with minimum Redundancy, Maximum Relevance (mRMR) and a new ensemble mRMR technique.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 mRMRe

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Sep 15;29(18):2365-8. doi: 10.1093/bioinformatics/btt383. Epub 2013 Jul 3.
mRMRe: an R package for parallelized mRMR ensemble feature selection.
De Jay N, Papillon-Cavanagh S, Olsen C, El-Hachem N, Bontempi G, Haibe-Kains B.

Rehh 1.13 – Search for Footprints of Selection using Haplotype Homozygosity based tests

Rehh 1.13

:: DESCRIPTION

Rehh is an R package to search for footprints of selection using Haplotype Homozygosity based tests

::DEVELOPER

Centre de Biologie et Gestion des Populations (CBGP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  MacOsX / Linux
  • R

:: DOWNLOAD

 Rehh

:: MORE INFORMATION

Citation

rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure.
Gautier M, Vitalis R.
Bioinformatics. 2012 Apr 15;28(8):1176-7. doi: 10.1093/bioinformatics/bts115.

IMPACT_S 1.0.0 – Integrated Multiprogram Platform to Analyze and Combine Tests of Selection

IMPACT_S 1.0.0

:: DESCRIPTION

IMPACT_S is a java swing based Graphical User Interface program for analyzing and/or combining several selection results from programs like, PAML (codeml), Datamonkey, TreeSAAP. Provides 3D homology modeling through Swiss Model and 3D mapping of selection results through Jmol.

::DEVELOPER

IMPACT_S team

:: SCREENSHOTS

IMPACT_S

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 IMPACT_S

:: MORE INFORMATION

Citation

Emanuel Maldonado, Kartik Sunagar, Daniela Almeida, Vitor Vasconcelos and Agostinho Antunes
IMPACT_S: Integrated Multiprogram Platform to Analyze and Combine Tests of Selection
PLoS ONE (2014) 9(10): e96243 DOI: 10.1371/journal.pone.0096243

FINEMAP 1.0 – Efficient Variable Selection using summary data from Genome-wide Association Studies

FINEMAP 1.0

:: DESCRIPTION

FINEMAP is a computationally efficient program for fine-mapping in genomic regions associated with complex diseases and traits via a shotgun stochastic search algorithm (Hans et al., 2007).

::DEVELOPER

 

Christian Benner

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux

:: DOWNLOAD

 FINEMAP

:: MORE INFORMATION

Citation

FINEMAP: Efficient variable selection using summary data from genome-wide association studies.
Benner C, Spencer CC, Havulinna AS, Salomaa V, Ripatti S, Pirinen M.
Bioinformatics. 2016 Jan 14. pii: btw018.

CLASS 2.1.2 – Constraint-based Local Assembly and Selection of Splice Variants

CLASS 2.1.2

:: DESCRIPTION

CLASS is a software tool  for accurately assembling splice variants using local read coverage patterns of RNA-seq reads, contiguity constraints from read pairs and spliced reads, and optionally information about gene structure extracted from cDNA sequence databases.

::DEVELOPER

Li Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsx/Linux

:: DOWNLOAD

 CLASS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 5:S14. doi: 10.1186/1471-2105-14-S5-S14. Epub 2013 Apr 10.
CLASS: constrained transcript assembly of RNA-seq reads.
Song L, Florea L.

Fizzy v1.4 – Feature Selection for Biological Data Formats

Fizzy v1.4

:: DESCRIPTION

Fizzy is a feature subset selection tool that uses FEAST in the background to run feature selection on biological data formats.

::DEVELOPER

Drexel’s EESI Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • Python

:: DOWNLOAD

 Fizzy

:: MORE INFORMATION

Citation

Fizzy: feature subset selection for metagenomics.
Ditzler G, Morrison JC, Lan Y, Rosen GL.
BMC Bioinformatics. 2015 Nov 4;16:358. doi: 10.1186/s12859-015-0793-8.

EFC-FCBF – Framework for Feature Construction and Selection for Improved Recognition of Antimicrobial Peptides

EFC-FCBF

:: DESCRIPTION

EPC (Evolutionary Feature Construction) is a method for prediction of Antimicrobial Peptides by proposing more complex sequence-based features that are able to capture information about local and distal patterns within a peptide.

::DEVELOPER

Computational Biology lab, George Mason University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • BioJava

:: DOWNLOAD

 EFC

:: MORE INFORMATION

Citation

Daniel Veltri, Uday Kamath, and Amarda Shehu.
“Improved Prediction of Antimicrobial Peptides Through Distal Sequence-based Features.”
ACM BCB, 2014 (under review).

BMGE 1.12 – Selection of Phylogenetic Informative Regions from Multiple Sequence Alignments

BMGE 1.12

:: DESCRIPTION

BMGE (Block Mapping and Gathering using Entropy) is a program that selects regions in a multiple sequence alignment that are suited for phylogenetic inference.

::DEVELOPER

Alexis Criscuolo (alexis.criscuolo@pasteur.fr), Simonetta Gribaldo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Java

:: DOWNLOAD

 BMGE

:: MORE INFORMATION

Citation

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments.
Criscuolo A, Gribaldo S.
BMC Evol Biol. 2010 Jul 13;10:210. doi: 10.1186/1471-2148-10-210.

ModelGenerator 0.851 – Amino Acid & Nucleotide Substitution Model Selection

ModelGenerator 0.851

:: DESCRIPTION

ModelGenerator is a model selection program that selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments. ModelGenerator supports 56 nucleotide and 96 amino acid substitution models.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

ModelGenerator

:: MORE INFORMATION

Citation:

Thomas M Keane, Christopher J Creevey ,Melissa M Pentony, Thomas J Naughton and James O McInerney (2006)
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified,
BMC Evolutionary Biology, 6:29