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

FastTagger 1.0 – Genome-Wide Tag SNP selection

FastTagger 1.0

:: DESCRIPTION

FastTagger is a software to calculate multi-marker tagging rules and select tag SNPs based on multi-marker LD. FastTagger uses several techniques to reduce running time and memory consumption.

::DEVELOPER

Limsoon Wong Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux/ Windows
  • C++ Compiler

:: DOWNLOAD

 FastTagger

:: MORE INFORMATION

Citation:

Guimei Liu, Yue Wang, Limsoon Wong.
FastTagger: An Efficient Algorithm for Genome-Wide Tag SNP selection using multi-marker linkage disequilibrium
BMC Bioinformatics, 11:66, February 2010.

BANFF 2.0 – Gene Network Feature Selection

BANFF 2.0

:: DESCRIPTION

BANFF (Bayesian Network Feature Finder) is an R package for gene network feature selection.

::DEVELOPER

Tianwei Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

BANFF

:: MORE INFORMATION

Citation

Bayesian network feature finder (BANFF): an R package for gene network feature selection.
Lan Z, Zhao Y, Kang J, Yu T.
Bioinformatics. 2016 Dec 1;32(23):3685-3687.

care 1.1.10 – High-Dimensional Regression and CAR Score Variable Selection

care 1.1.10

:: DESCRIPTION

The “care” package a novel multivariate algorithm for large scale SNP selection using CAR score regression, a promising new approach for prioritizing biomarkers.  CAR scores measure the correlation between the response and the Mahalanobis-decorrelated predictors. The squared CAR score is a natural measure of variable importance and provides a canonical ordering of variables. This package provides functions for estimating CAR scores, for variable selection using CAR scores, and for estimating corresponding regression coefficients. Both shrinkage as well as empirical estimators are available.

::DEVELOPER

Strimmer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 care

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2012 Oct 31;13:284. doi: 10.1186/1471-2105-13-284.
A novel algorithm for simultaneous SNP selection in high-dimensional genome-wide association studies.
Zuber V, Duarte Silva AP, Strimmer K.

SLR 1.4.3 – Sitewise Likehood Ratio Estimation of Selection

SLR 1.4.3

:: DESCRIPTION

SLR (Sitewise Likehood Ratio) is a program to detect sites in coding DNA that are unusually conserved and/or unusually variable (that is, evolving under purify or positive selection) by analysing the pattern of changes for an alignment of sequences on an evolutionary tree. The strength of selection at each site is determined by comparing the rate of nonsynonymous (amino acid changing) substitutions to that of synonymous (silent) substituions, the latter assumed to be invisible to selection and so evolving in a strictly neutral fashion.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 SLR

:: MORE INFORMATION

Citation:

Genetics. 2005 Mar;169(3):1753-62. Epub 2005 Jan 16.
Detecting amino acid sites under positive selection and purifying selection.
Massingham T, Goldman N.

DetSel 1.0.3 – Detect Markers Responding to Selection

DetSel 1.0.3

:: DESCRIPTION

DetSel is an R package to detect markers responding to selection

::DEVELOPER

Centre de Biologie et Gestion des Populations (CBGP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  MacOsX / Linux
  • R

:: DOWNLOAD

 DetSel

:: MORE INFORMATION

Citation

J Hered. 2003 Sep-Oct;94(5):429-31.
DetSel 1.0: a computer program to detect markers responding to selection.
Vitalis R1, Dawson K, Boursot P, Belkhir K.

Rehh 3.0.1 – Search for Footprints of Selection using Haplotype Homozygosity based tests

Rehh 3.0.1

:: 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.

Gblocks 0.91b – Selection of Conserved Blocks from multiple alignments for their use in Phylogenetic Snalysis

Gblocks 0.91b

:: DESCRIPTION

Gblocks is a computer program written in C that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis.

::DEVELOPER

Castresana Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX

:: DOWNLOAD

  Gblocks

:: MORE INFORMATION

Citation:

Talavera, G., and Castresana, J. (2007).
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.
Systematic Biology 56, 564-577.

TreeSAAP 3.2 – Selection of Amino Acid Properties using Phylogenetic Trees model

TreeSAAP 3.2

:: DESCRIPTION

TreeSAAP (Selection of Amino Acid Properties Based on Phylogenetic Trees) measures the selective influences on 31 structural and biochemical amino acid properties during phylogenesis (the history of genealogical development) and performs goodness-of-fit and categorical statistical tests.

::DEVELOPER

McClellan, David

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

TreeSAAP

:: MORE INFORMATION

Citation

TreeSAAP: selection on amino acid properties using phylogenetic trees.
Woolley S, Johnson J, Smith MJ, Crandall KA, McClellan DA.
Bioinformatics. 2003 Mar 22;19(5):671-2