:: DESCRIPTION
BANFF (Bayesian Network Feature Finder) is an R package for gene network feature selection.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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
