Software

Association analysis

Linkage analysis

Pedigree

Segregation analysis

Utilities

famFLM

• full name:
• version:
• descriptions: Region-based association test for familial data under functional linear models.
• keywords: association analysis, gene-based mapping, functional data analysis, family data
• authors: Gulnara Svishcheva and Nadezhda Belonogova
• web: http://mga.bionet.nsc.ru/soft/famFLM/
• source code language: R
• operating systems: Linux, Windows

FREGAT

• full name:
• version: 1.0
• descriptions:
• keywords: association analysis, family data, region/gene-based mapping, kernal-based regration, functional data analysis, burden test, multiple regretion
• authors: Gulnara Svishcheva and Nadezhda Belonogova
• web: http://mga.bionet.nsc.ru/soft/FREGAT/
• source code language: R
• operating systems: Linux, Windows

FFBSKAT

• full name:
• version: 1.0
• descriptions: Software for region/gene association analysis of quantitative traits in samples of related individuals. The software is an implementation of the method based on the kernel machine regression approach described by Schifano et al.
• keywords: association analysis, region/gene-based mapping, kernal-based regration, family data
• authors: Gulnara Svishcheva and Nadezhda Belonogova
• web: http://mga.bionet.nsc.ru/soft/FFBSKAT/
• source code language: R
• operating systems: Linux, Windows

GenABEL

• full name: GenABEL
• version: 1.8-0
• descriptions: R library for genome-wide association analysis
• keywords: association analysis
• authors: Y. Aulchenko
• web: http://www.genabel.org/
• source code language: R, C
• operating systems: Linux, Windows
• reference: Aulchenko Y., Ripke S., Isaacs A., van Duijn C. (submitted) GenABEL: a R library for genome-wide association analysis

miLD and booLD

• full name: MultIallelic Linkage Disequilibrium (LD) and bootstrap LD
• version: miLD v 2.1 and booLD v 1.1
• descriptions: unbiased estimation of multi-allelic D'
• keywords: association analysis
• authors: Y. Aulchenko
• web: http://mga.bionet.nsc.ru/soft/miLD_and_booLD/booLD-1.1.tar.gz
• web: http://mga.bionet.nsc.ru/soft/miLD_and_booLD/miLD-2.1.tar.gz
• source code language: Perl, FORTRAN
• operating systems: Linux, Cygwin

cvcrF2

• full name:
• version: 0.9b
• descriptions: A set of programs from MGA and other people arranged in the form of package for combined variance components/regression QTL analysis in F-2 progeny coming freom crosses between outbred lines
• authors: Yurii Aulchenko
• keywords: linkage analysis
• web: http://mga.bionet.nsc.ru/soft/cvcrf2/cvcrF2-0.9b.tar.gz
• source code language: FORTRAN
• operating systems: Linux
• reference:

GADS

• full name:
• version: 1.1
• descriptions: Software for Genetic Analyses of quantitative traits Distributed with Spike on the base of large pedigrees without loops
• keywords: parametric linkage analysis, non-normal destribution
• authors: Tatiana Axenovich
• web: http://mga.bionet.nsc.ru/soft/GADS/GADS-1.1.tar.gz
• source code language: Perl, FORTRAN
• operating systems: Linux, Windows

MGA-MAPF2

• full name:
• version:
• descriptions: A simple, thou powerful and easy to modificate Fortran program to map QTLs in F-2 intercross in model organisms
• keywords: linkage analysis
• authors: Yurii Aulchenko
• web: http://mga.bionet.nsc.ru/soft/mgamapf2/
• source code language: FORTRAN
• operating systems: Windows
• reference:

MGA-SIMULATE

• full name:
• version:
• descriptions: A program package for simulating genotypes and phenotypes given a pedigree structure, genetic map and a model of inheritance. For a pedigree founders, it is possible to come from 2 different populations (breeds). MGA-SIMULATE-00.06 - a newer version of MGA-SIMULATE
• keywords: linkage analysis
• authors: Yurii Aulchenko
• web: http://mga.bionet.nsc.ru/soft/simulate/
• source code language: C, C++, FORTRAN
• operating systems: Linux
• reference:

MQscore

• full name: MQscore
• version: 1.0
• descriptions: A program for parametric linkage analysis of quantitative traits on the base of large pedigrees without loops.
• keywords: parametric linkage analysis, polyallelic markers, quantitative traits
• authors: Tatiana Axenovich
• web: MQscore home page
• source code language: FORTRAN, Perl
• operating systems: Linux, Windows

MQscore_SNP

• full name: MQscore_SNP
• version: 1.1
• descriptions: A program for multipoint parametric linkage analysis of quantitative traits and SNP markers on the base of large pedigrees without loops.
• keywords: parametric linkage analysis, biallelic markers, quantitative traits
• authors: Tatiana Axenovich
• web: MQscore_SNP home page
• source code language: FORTRAN, Perl
• operating systems: Linux, Windows

fcn

• full name:
• version:
• descriptions: A program for describing complex pedigree structures.
• keywords: pedigree
• authors: F. Liu, S. Elefante, C.M.van Duijn, Y.S.Aulchenko
• web: http://mga.bionet.nsc.ru/soft/fcn/
• source code language: Perl
• operating systems:
• reference:

LOOP_EDGE

• full name:
• version:
• descriptions: A program for cutting and extension of pedigrees with multiple loops. The classical Kruskal algorithm was used in the package.
• keywords: pedigree, breaking loops, Kruskal algorithm
• authors: Tatiana Axenovich
• web: http://mga.bionet.nsc.ru/soft/LOOP/LOOP_EDGE.tar.gz
• source code language: FORTRAN
• operating systems: Windows, Linux, Linux with MPI
• reference:

LOOP_PED

• full name:
• version:
• descriptions: A program for cutting and extension of pedigrees with multiple loops. Algorithm based on the step by step breaking loops was used in the package.
• keywords: pedigree, breaking loops, step by step algorithm
• authors: Tatiana Axenovich
• web: http://mga.bionet.nsc.ru/soft/LOOP/LOOP_PED.tar.gz
• source code language: FORTRAN
• operating systems: Windows, Linux
• reference:

LOOP_STAR

• full name:
• version:
• descriptions: A program for cutting and extension of pedigrees with multiple loops. Algorithm described by Vitezica et al, HumHered 2004,57:1-9, was used in the package.
• keywords: pedigree, breaking loops, Vitezica algorithm
• authors: Tatiana Axenovich
• web: http://mga.bionet.nsc.ru/soft/LOOP/LOOP_STAR.tar.gz
• source code language: FORTRAN
• operating systems: Windows, Linux
• reference:

MGA-UTIL

• full name:
• version:
• descriptions: A set of utilities for pedigrees (check errors, renumber, etc...) developed at Lab of MGA.
• keywords: pedigree
• authors:
• web: http://mga.bionet.nsc.ru/soft/mga-util/
• source code language: FORTRAN, C++
• operating systems: Linux
• reference:

PedCut

• full name: PedCut
• version: 1.19
• descriptions: A program for cutting complex pedigree into computable sub-pedigrees with user-specified MaxBit size
• keywords: pedigree
• authors: F. Liu
• web: http://mga.bionet.nsc.ru/soft/pedcut/pedcut_1.19.tar.gz
• source code language: Perl; the program uses PEDIG (Fortran-77) and PedHunter (C) software
• operating systems: Linux, Cygwin
• reference: F. Liu et al., in preparation

PedigreeQuery

• full name:
• version:
• descriptions: A program for drawing pedigrees step-by-step.
• keywords: pedigree
• authors: Anatoly Kirichenko
• web: http://mga.bionet.nsc.ru/soft/pedquery/pedigreequery.html
• source code language: Java
• operating systems:
• reference:

PedPeel

• full name: PedPeel
• version: 0.0.4
• descriptions: A program for preparing pedigree data for calculation of Elston-Stewarts' likelihood function. It finds an optimal way to peel.
• keywords: pedigree, optimal likelihood culculation
• authors: Nadezhda Belonogova
• web: PedPeel home page
• source code language: Perl
• operating systems: Linux, Windows

PedStr

• full name: Pedigree strip
• version: PedStr_H and PedStr_L
• descriptions: A program for splitting large pedigree into smaller subpedigrees.
• keywords: pedigree
• authors: Anatoly V Kirichenko
• web: http://mga.bionet.nsc.ru/soft/PedStr/PedStr.tar.gz
• source code language: FORTRAN-77
• operating systems: Linux, Windows

MAIA

• full name:
• version: 1.0
• descriptions: A program for complex segregation analysis in animals. Allow analysis of pedigrees where founders come from two different populations (breeds)
• keywords: segregation analysis, animals, between population crosses
• authors: Yurii Aulchenko
• web: http://mga.bionet.nsc.ru/soft/maia-1.0/
• source code language: FORTRAN
• operating systems: Windows
• reference:

MAN-A1

• full name:
• version:
• descriptions: A program for complex segregation analysis in humans
• keywords: segregation analysis, humans, binary traits
• authors:
• web: http://mga.bionet.nsc.ru/soft/MAN/MAN.zip
• source code language: FORTRAN
• operating systems: Windows
• reference:

MAN_H_PG

• full name:
• version: 3.0
• descriptions: Software for complex segregation analysis of quantitative traits on large pedigrees without loops
• keywords: segregation analysis, humans, quantitative traits
• authors: Tatiana Axenovich
• web: http://mga.bionet.nsc.ru/soft/MAN_H_PG/MAN_H_PG.tar.gz
• source code language: Perl, FORTRAN
• operating systems: Linux, Windows

affy2mega

• full name:
• version:
• descriptions: A program for converting Affymetrix SNP output data files, as written in text format, to mega2 or merlin format.
• keywords:
• authors: Yurii Aulchenko
• web: http://mga.bionet.nsc.ru/soft/affy2mega/
• source code language: Perl
• operating systems:
• reference:

desc_sta

• full name:
• version:
• descriptions: A program for making basic descriptive statistics for samples from the normal distribution.
• keywords:
• authors: Yurii Aulchenko
• web: http://mga.bionet.nsc.ru/soft/desc_sta/
• source code language: C++
• operating systems: Windows
• reference:

gen_qc

• full name:
• version:
• descriptions: A program for preparing input data for PedCheck.
• keywords:
• authors: Irina Zorkoltseva
• web: http://mga.bionet.nsc.ru/soft/gen_qc/
• source code language: Perl
• operating systems:
• reference:

Loki_QTLc

• full name:
• version: 1.02
• descriptions: A set of programs for MCMC calculations of QTL-coefficients. Majority of source code is Loki 2.3 by S. Heath, which should be downloaded from our FTP or elsewhere.
• keywords:
• authors: Yurii Aulchenko
• web: http://mga.bionet.nsc.ru/soft/Loki_QTLc/
• source code language: C, FORTRAN
• operating systems: Linux
• reference:

manfreq

• full name:
• version: 1.0
• descriptions: A program for estimation of allelic frequencies in ancestral populations.
• keywords:
• authors:
• web: http://mga.bionet.nsc.ru/soft/manfreq/
• source code language: Windows
• operating systems:
• reference:

METHGI

• full name:
• version:
• descriptions: A set of subroutines for maximization of multi parametric function.
• keywords:
• authors: Tatiana Axenovich, Yurii Aulchenko
• web: http://mga.bionet.nsc.ru/soft/methgi/methgi.html
• source code language: Fortran-77, Fortran-90 and C++
• operating systems: Linux
• reference:

MitPene

• full name:
• version:
• descriptions: A program for analysis of mitohondrial diseases.
• keywords:
• authors: Anatoly Kirichenko
• web: http://mga.bionet.nsc.ru/soft/mitpene/mitpene.html
• source code language: C++
• operating systems: Windows
• reference:

Ped_Outlier

• full name:
• version: 1.1
• descriptions: Software for detecting within-family outliers
• keywords:
• authors: Irina Zorkoltseva
• web: http://mga.bionet.nsc.ru/soft/ped_outlier/Ped_Outlier-1.1.tar.gz
• source code language: FORTRAN
• operating systems: Linux, Windows

pool_str

• full name:
• version:
• descriptions: A program for pooling STR data coming from different genotyping experiments.
• keywords:
• authors: Yurii Aulchenko
• web: http://mga.bionet.nsc.ru/soft/pool_str/pool_str-1.1.tar.gz
• source code language: Perl, C++
• operating systems: Cygwin, Linux
• reference:

recode_gen

• full name:
• version:
• descriptions: A program for recoding alphabeticly coded systems into numerical alleles for PedCheck.
• keywords:
• authors: Irina Zorkoltseva
• web: http://mga.bionet.nsc.ru/soft/recodesnp/recodesnp.tar.gz
• source code language: Perl
• operating systems:
• reference:

recode_ped

• full name:
• version:
• descriptions: A program for verification of pedigree data and recoding pedigrees from free format to standard format.
• keywords:
• authors: Tatiana Axenovich
• web: http://mga.bionet.nsc.ru/soft/recode_ped/recode_ped.tar.gz
• source code language: Perl
• operating systems:
• reference:

Last modified: 23 October 2015
by Anatoly Kirichenko