MIXMUL – Estimating Haplotype Frequencies and Reconstructing Haplotypes from Mixed Genotype Data

MIXMUL

:: DESCRIPTION

MIXMUL (Mixture of Weighted Multinomial) procedure is a convenient haplotype inference tool for mixed data to estimate haplotype frequencies accurately and output the most likely reconstructed haplotype pairs of each subject in the estimation.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package

:: DOWNLOAD

 MIXMUL

:: MORE INFORMATION

Citation

J Biomed Sci. 2009 Jun 2;16:52. doi: 10.1186/1423-0127-16-52.
A novel tool for individual haplotype inference using mixed data.
Lin CP, Fann CS.

HapMDR – Detection of Haplotype-haplotype Interaction

HapMDR

:: DESCRIPTION

HapMDR is a convenient analysis tool for detecting disease-related haplotype-haplotype interactions. HapMDR overcome high-dimensional issues which combine the advantages of data mining with the concept of haplotypes and consider haplotype uncertainty.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R package

:: DOWNLOAD

 HapMDR

:: MORE INFORMATION

hapCART – Detect Interactions among Haplotypes in Association with a Disease

hapCART

:: DESCRIPTION

HapCART is a convenient analysis tool for detecting disease-related haplotype-haplotype interactions. HapCART overcome high-dimensional issues which combine the advantages of data mining with the concept of haplotypes and consider haplotype uncertainty.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R package

:: DOWNLOAD

  HapCART

:: MORE INFORMATION

MSS v1 – Analysis of Genome-wide Association Data

MSS v1

:: DESCRIPTION

MSS (Maximal Segmental Score) is an R program for the analysis of genome-wide association data

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • R package

:: DOWNLOAD

 MSS

:: MORE INFORMATION

Citation

Using maximal segmental score in genome-wide association studies.
Lin YC, Hsiao CL, Hsieh AR, Lian IeB, Fann CS.
Genet Epidemiol. 2012 Sep;36(6):594-601. doi: 10.1002/gepi.21652.

MicroFamily 1.2 – Detect Flanking Region Similarities among different Microsatellite Loci

MicroFamily 1.2

:: DESCRIPTION

MicroFamily is a program designed for identifying flanking region similarities between different microsatellite sequences obtained from screening partial genomic libraries.

::DEVELOPER

Emese Meglécz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MicroFamily

:: MORE INFORMATION

Citation

Meglécz, E. 2007.
MicroFamily: A computer program for detecting flanking region similarities among different microsatellite loci.
Molecular Ecology Notes 7 : 18-20

GP 0.26 / Arka 0.11 – Sequence Manipulation tools

GP 0.26 / Arka 0.11

:: DESCRIPTION

GP and Arka are very leightweighed programs for manipulation of DNA / RNA / protein sequences. They are designed on one hand to run smoothly on older machines, and on the other — to faciliate processing of large numbers of sequence / data files. GP includes utilities to convert DNA / RNA to protein, determine codon usage / GC contents, promotor searches, Tm, searching for restriction sites, converting sequences into numerical representations and much more.

::DEVELOPER

Dr. January Weiner 3rd

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GP  / Arka

:: MORE INFORMATION

Ped-sim v1.3.5 – Pedigree Simulator

Ped-sim v1.3.5

:: DESCRIPTION

Ped-sim enables simulations of data for individuals from a given pedigree structure. It can use sex-specific genetic maps to incorporate differences in male and female recombination events.

::DEVELOPER

Williams lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Ped-sim

:: MORE INFORMATION

Citation:

Caballero M, Seidman DN, Qiao Y, Sannerud J, Dyer TD, Lehman DM, Curran JE, Duggirala R, Blangero J, Carmi S, Williams AL.
Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives.
PLoS Genet. 2019 Dec 20;15(12):e1007979. doi: 10.1371/journal.pgen.1007979. PMID: 31860654; PMCID: PMC6944377.

Hapi 1.03 – Rapid Haplotype Inference for Nuclear Families

Hapi 1.03

:: DESCRIPTION

Hapi is a program that efficiently infers minimum recombinant and maximum likelihood haplotypes for nuclear families.

::DEVELOPER

Williams lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Hapi

:: MORE INFORMATION

Citation:

Genome Biol. 2010;11(10):R108. doi: 10.1186/gb-2010-11-10-r108. Epub 2010 Oct 29.
Rapid haplotype inference for nuclear families.
Williams AL, Housman DE, Rinard MC, Gifford DK.

CodABC 2.0.0b – Coestimation of Recombination, Substitution and Molecular Adaptation Rates by Approximate Bayesian Computation

CodABC 2.0.0b

:: DESCRIPTION

The package CodABC is computer framework to coestimate Recombination, Substitution and Molecular Adaptation (dN/dS) rates by approximate Bayesian computation from coding sequence alignments.

::DEVELOPER

Dr. MIGUEL ARENAS

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

  CodABC

:: MORE INFORMATION

Citation

Mol Biol Evol. 2015 Apr;32(4):1109-12. doi: 10.1093/molbev/msu411. Epub 2015 Jan 9.
CodABC: A Computational Framework to Coestimate Recombination, Substitution, and Molecular Adaptation Rates by Approximate Bayesian Computation.
Arenas M, Lopes JS, Beaumont MA, Posada D

Exit mobile version