Tag: Imputing

E-MAPs 1.1 – Imputing Quantitative Genetic Interactions

E-MAPs 1.1

:: DESCRIPTION

E-MAPs (Epistatic miniarray profiles) are a high-throughput approach capable of quantifying aggravating or alleviating genetic interactions between gene pairs. The datasets resulting from E-MAP experiments typically take the form of a symmetric pairwise matrix of interaction scores. These datasets have a significant number of missing values – up to 35% – that can reduce the effectiveness of some data analysis techniques and prevent the use of others.

::DEVELOPER

the Machine Learning Group (MLG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /Mac OsX
  • Python

:: DOWNLOAD

 E-MAPs

:: MORE INFORMATION

Citation

Missing value imputation for epistatic MAPs
Colm Ryan , Derek Greene , Gerard Cagney and Pádraig Cunningham
BMC Bioinformatics 2010, 11:197 doi:10.1186/1471-2105-11-197

AlphaPlantImpute – Phasing and Imputing Genotype data in Plant Breeding Populations

AlphaPlantImpute

:: DESCRIPTION

AlphaPlantImpute is a software package designed for phasing and imputing genotype data in plant breeding populations. AlphaPlantImpute can be implemented within and across bi-parental populations to phase and impute focal individuals genotyped at low-density to high-density. Focal individuals can be descendants of a bi-parental cross at various levels of selfing or can be parents of one or more bi-parental populations. All information on the model of analysis, input files and their layout, is specified in a single parameter file.

::DEVELOPER

AlphaGenes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

AlphaPlantImpute

:: MORE INFORMATION

Citation

Gonen S, Wimmer V, Gaynor RC, Byrne E, Gorjanc G, Hickey JM.
A heuristic method for fast and accurate phasing and imputation of single-nucleotide polymorphism data in bi-parental plant populations.
Theor Appl Genet. 2018 Nov;131(11):2345-2357. doi: 10.1007/s00122-018-3156-9. Epub 2018 Aug 4. PMID: 30078163; PMCID: PMC6208939.

AlphaPeel 0.1.0 – Calling, Phasing, and Imputing Genotype and Sequence data in Pedigree Populations

AlphaPeel 0.1.0

:: DESCRIPTION

AlphaPeel is a software package for calling, phasing, and imputing genotype and sequence data in pedigree populations. This program implements single locus peeling, multi locus peeling, and hybrid peeling.

::DEVELOPER

AlphaGenes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

AlphaPeel

:: MORE INFORMATION

Citation

Whalen A, Ros-Freixedes R, Wilson DL, Gorjanc G, Hickey JM.
Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees.
Genet Sel Evol. 2018 Dec 18;50(1):67. doi: 10.1186/s12711-018-0438-2. PMID: 30563452; PMCID: PMC6299538.

AlphaImpute 1.9.8.3 – Imputing and Phasing Genotype data in Populations

AlphaImpute 1.9.8.3

:: DESCRIPTION

AlphaImpute is a software package for imputing and phasing genotype data in populations with pedigree information. AlphaImpute combines long range phasing with segregation analysis and haplotype library imputation (SAHLI) methodology to impute alleles and genotypes.

::DEVELOPER

AlphaGenes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 AlphaImpute

:: MORE INFORMATION

Citation

Genet Sel Evol. 2013 Apr 25;45:10. doi: 10.1186/1297-9686-45-10.
Extending long-range phasing and haplotype library imputation methods to impute genotypes on sex chromosomes.
Hickey JM1, Kranis A.