HapYDive – Excel Plugin for Y-STR Haplotype Diversity Calculation

HapYDive

:: DESCRIPTION

HapYDive is a software for Y-STR haplotype diversity calculation.This program allows fast and reliable determination of which Y-STRs are the most informative by evaluating all possible combinations.With the HapYDive it is possible to analyse any set of Y markers up to a maximum of 20, with a minimum number of 4 markers fixed for calculations. Results on the application of this program to different population samples and sizes and with a certain combination of Y-STR markers are presented and discussed, together with its usefulness mainly to the forensic community.

::DEVELOPER

Filipe Pereira

:: SCREENSHOTS

: REQUIREMENTS

  • Windows
  • Excel

:: DOWNLOAD

HapYDive

:: MORE INFORMATION

Citation

Alves C, Gusmão L, Meirinhos J, Amorim A (2006)
Making the most of Y-STR haplotypes. The HapYDive.
Forensic Genetics 11: 201-203.

MAGI – Mutation Annotation & Genome Interpretation

MAGI

:: DESCRIPTION

MAGI is a publicly available web application to explore and annotate cancer genomics data.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

MAGI

:: MORE INFORMATION

Citation:

MAGI: visualization and collaborative annotation of genomic aberrations.
Leiserson MD, Gramazio CC, Hu J, Wu HT, Laidlaw DH, Raphael BJ.
Nat Methods. 2015 May 28;12(6):483-4. doi: 10.1038/nmeth.3412.

RAIG 1.0.2 – Identifying Recurrent and Independent Copy Number Aberration

RAIG 1.0.2

:: DESCRIPTION

RAIG ( Recurrent Aberrations from Interval Graph) is a combinatorial approach to the problem of identifying independent and recurrent copy number aberrations, focusing on the key challenging of separating the overlaps in aberrations across individuals into independent events.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 RAIG

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Jun 15;30(12):i195-i203. doi: 10.1093/bioinformatics/btu276.
Detecting independent and recurrent copy number aberrations using interval graphs.
Wu HT, Hajirasouliha I, Raphael BJ.

MultiBreak-SV – Detect Structural Variants from Single Molecule Sequencing data

MultiBreak-SV

: DESCRIPTION

MultiBreak-SV is a software for structural variation analysis from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 MultiBreak-SV

:: MORE INFORMATION

Citation:

Characterization of Structural Variants with Single Molecule and Hybrid Sequencing Approaches.
Ritz A, Bashir A, Sindi S, Hsu D, Hajirasouliha I, Raphael BJ.
Bioinformatics. 2014 Oct 28. pii: btu714.

mosaic 0.1-1 – Hybrid Zones Analysis

mosaic 0.1-1

:: DESCRIPTION

Mosaic is a software which calculates the ‘mosaicity’ of a one dimensional hybrid zone. This package uses likelihood to fit step-wise models to one dimensional hybrid zone data, and to estimate the ‘mosaicity’ of the hybrid zone.

::DEVELOPER

Rich FitzJohn , Leithen M’Gonigle

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • R package

:: DOWNLOAD

  Mosaic

:: MORE INFORMATION

Citation

Evolution. 2010 Feb 1;64(2):444-55. doi: 10.1111/j.1558-5646.2009.00838.x. Epub 2009 Sep 23.
Assortative mating and spatial structure in hybrid zones.
M’Gonigle LK, FitzJohn RG.

FSuite 1.0.4 – Exploiting Inbreeding in dense SNP chip and Exome data

FSuite 1.0.4

:: DESCRIPTION

FSuite is an integrative solution to exploit inbreeding in dense SNP chip and exome data. Its goals are for

  1. Population genetic studies:

    • estimating and detecting inbreeding on individuals without known genealogy,

    • estimating the individual probability to be into offspring of different mating types,

    • estimating the proportion of mating types in the population,

  2. Rare disease studies: performing homozygosity mapping with heterogeneity,

  3. Multifactorial disease studies: performing HBD-GWAS strategy.

::DEVELOPER

FSuite team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX

:: DOWNLOAD

FSuite

:: MORE INFORMATION

Citation

Gazal S, Sahbatou M, Babron MC, Génin E, Leutenegger AL.
FSuite: exploiting inbreeding in dense SNP chip and exome data.
Bioinformatics. 2014 Jul 1;30(13):1940-1. doi: 10.1093/bioinformatics/btu149. Epub 2014 Mar 14. PMID: 24632498.

MQLS 1.5 – Case-Control Association Testing with Related Individuals

MQLS 1.5

:: DESCRIPTION

MQLS (More Powerful Quasi-Likelihood Score Test)can handle arbitrary number of markers and samples and have other features that we found useful in our studies, such as pedigree checking and input/output formats. In addition to genotyped markers, this version can carry out association tests using imputed allele counts (“dosages”) generated by MACH and an empirical variance estimator.

::DEVELOPER

Liming Liang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • C Compier

:: DOWNLOAD

  MQLS

:: MORE INFORMATION

Reference

Thornton T., McPeek M. S. (2007)
Case-Control Association Testing with Related Individuals: A More Powerful Quasi-Likelihood Score Test.
Am J Hum Genet, 81, 321-337.

FEstim 1.3.2 – Estimation of the Inbreeding Coefficient of Individuals

FEstim 1.3.2

:: DESCRIPTION

FEstim is a software for estimation of the inbreeding coefficient of individuals through use of a dense map of genetic markers and computation of genomically controlled homozygosity mapping lodscores.

::DEVELOPER

FEstim team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX

:: DOWNLOAD

 FEstim

:: MORE INFORMATION

Citation

Am J Hum Genet. 2006 Jul;79(1):62-6. Epub 2006 Apr 28.
Using genomic inbreeding coefficient estimates for homozygosity mapping of rare recessive traits: application to Taybi-Linder syndrome.
Leutenegger AL, Labalme A, Genin E, Toutain A, Steichen E, Clerget-Darpoux F, Edery P.

GSM 0.3 – Genotype-based Matching

GSM 0.3

:: DESCRIPTION

GSM (genetic similarity score matching)is a software for efficient matched analysis of cases and controls in a genome-wide or large-scale candidate gene association study. GSM comprises three steps: (1) calculating similarity scores for pairs of individuals using the genotype data; (2) matching sets of cases and controls based on the similarity scores so that matched cases and controls have similar genetic background; and (3) using conditional logistic regression to perform association tests. Through computer simulation we show that GSM correctly controls false-positive rates and improves power to detect true disease predisposing variants

::DEVELOPER

Liming Liang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows

:: DOWNLOAD

 GSM

:: MORE INFORMATION

Citation

Weihua Guan*, Liming Liang*, Michael Boehnke, Gonçalo R. Abecasis (2009).
Genotype-based matching to correct for population stratification in large-scale case-control genetic association studies.
Genet Epidemiol DOI:10.1002/gepi.20403

BestRepeat 1.0 – Variance Components Linkage Analysis with Repeated Measurements

BestRepeat 1.0

:: DESCRIPTION

BestRepeat is a R package to calculate the optimal number of repeated measures for quantitative trait linkage analysis.

::DEVELOPER

Liming Liang

 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BestRepeat

:: MORE INFORMATION

Citation

Liang L, Chen WM, Sham PC and Abecasis GR. (2009)
Variance Components Linkage Analysis with Repeated Measurements.
Human Heredity 67: 237-247.