:: DESCRIPTION
Fizzy is a feature subset selection tool that uses FEAST in the background to run feature selection on biological data formats.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
The program ProtEvol performs two kinds of computation.
::DEVELOPER
Unidad de Bioinformatica CBMSO
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Maximum likelihood phylogenetic inference with selection on protein folding stability.
Arenas M, Sánchez-Cobos A, Bastolla U.
Mol Biol Evol. 2015 Apr 2. pii: msv085.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
CONSEL is a program package consists of small programs written in C language. It calculates the probability value (i.e., p-value) to assess the confidence in the selection problem. Although CONSEL is applicable to any selection problem, it is mainly designed for the phylogenetic tree selection. CONSEL does not estimate the phylogenetic tree by itself, but CONSEL does read the output of the other phylogenetic packages, such as Molphy, PAML, PAUP*, TREE-PUZZLE, and PhyML. CONSEL calculates the p-value using several testing procedures; the bootstrap probability, the Kishino-Hasegawa test, the Shimodaira-Hasegawa test, and the weighted Shimodaira-Hasegawa test. In addition to these conventional tests, CONSEL calculates the p-value based on the approximately unbiased test using the multi-scale bootstrap technique.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Shimodaira, H. & Hasegawa, M.
CONSEL: for assessing the confidence of phylogenetic tree selection.
Bioinformatics 17, 1246-1247 (2001).
:: DESCRIPTION
ASSIE is a statistical model for inferring selection coefficients associated with coding variants in the human genome.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Huang YF, Siepel A.
Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease.
Genome Res. 2019 Aug;29(8):1310-1321. doi: 10.1101/gr.245522.118. Epub 2019 Jun 27. PMID: 31249063; PMCID: PMC6673719.
:: DESCRIPTION
SNPPicker is a post-processor to optimize the selection of tag SNPs from common bin-tagging programs. SNPPicker uses a multi-step search strategy in combination with a statistical model to produce optimal genotyping panels. SNPPicker’s algorithm is also designed to optimize tag SNP selection for multi-population panels. It accounts for several assay-specific constraints such as predicted assay failure of SNPs and avoidance of SNPs that are too close. The latter issue affects one third of all SNPs in the 1000 genomes project pilot 1 data.SNPPicker automates the design of tag SNP genotyping panels by maximizing the likelihood of successfully genotyping the selected SNPs while minimizing the number of tag SNPs to assay. Geno-typing success is a function of two properties: the genotyping probability of a bin (or cluster of bins) statistically derived from the individual genotyping probability of each SNP; and (for some platforms) the proximity distance between SNPs. The genotyping probabilities currently used by SNPPicker are derived a from pro-spective analysis of the performance of genotyping assay and the probability model can be updated or changed for other platforms. SNP proximity is a strictly enforced constraint
::DEVELOPER
Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2011 May 2;12:129.
SNPPicker: high quality tag SNP selection across multiple populations.
Sicotte H, Rider DN, Poland GA, Dhiman N, Kocher JP.
:: 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
:: DOWNLOAD
:: 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.
:: DESCRIPTION
PIMSA is an implementation of a reversible jump MCMC algorithm that samples across the space of all possible models in the context of variable selection.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
