Endog 4.8 – Analyse Pedigree Information

Endog 4.8

:: DESCRIPTION

ENDOG‘s Primary functions are the computation of the individual inbreeding (F) (Wright, 1931) and the average relatedness (AR) (Gutiérrez et al., 2003; Goyache et al., 2003) coefficients. Additionally, users can compute with ENDOG useful parameters in population genetics such as that described for Biochard et al. (1997) for the number of ancestors explaining genetic variability or those proposed by Robertson (1953) and Vassallo et al. (1996) for the genetic importance of the herds. ENDOG also can compute F statistics (Wright, 1978) from genealogical information following Caballero and Toro (2000; 2002). Moreover, the present version of ENDOG calculates effective population size following different methodologies including regression approaches and particularly the recently proposed realized effective population size from individual increase in inbreeding (Gutiérrez et al., 2008), modified to account for avoidance of self-fertilization (Gutiérrez et al., 2009).

::DEVELOPER

Juan Pablo Gutiérrez García

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Endog

:: MORE INFORMATION

Citation

A note on ENDOG: a computer program for analysing pedigree information.
Gutiérrez JP, Goyache F.
J Anim Breed Genet. 2005 Jun;122(3):172-6.

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.

LDWP – Linked Region Detection without Pedigree

LDWP

:: DESCRIPTION

LDWP (Linked Region Detection without Pedigree) is a software package for linkage analysis that finds the mutation regions for the case where the input individuals are closely related, but the pedigree is not known. A typical example is that in the pedigree below the individuals in the dotted rectangle are closely related,and the genotype data of them are known, whereas the genotype data of individuals outside the dotted rectangle are not available and even the pedigree may not be clear. LDWP takes the genotype data of the individuals in the dotted rectangle and the diagnoses (diseased or normal) information of each individual in the dotted rectangle as its input, and report the mutation regions.

::DEVELOPER

Lusheng Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 LDWP

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2012 Mar-Apr;9(2):499-510. doi: 10.1109/TCBB.2011.134
Mutation Region Detection for Closely Related Individuals without a Known Pedigree Using High-Density Genotype Data.
Ma W, Yang Y, Chen ZZ, Wang L.

LINKAGE – Pedigree Linkage Analysis

LINKAGE

:: DESCRIPTION

LINKAGE package is a series of programs for maximum likelihood estimation of recombination rates, calculation of lod score tables, and analysis of genetic risks. The analysis programs are divided into two groups. The first group can be used for general pedigrees with marker and disease loci. Programs in the second group are for three-generation families and codominant marker loci, and are primarily intended for the construction of genetic maps from data on reference families.

::DEVELOPER

Lab of Statistical Genetics, Rockefeller University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

 LINKAGE

:: MORE INFORMATION

SQTL – Semiparametric QTL Mapping in General Pedigrees

SQTL

:: DESCRIPTION

SQTL is a semiparametric quantitative trait loci mapping method to human gene expression data. The SQTL mapping method is rank-based and therefore robust to non-normality and outliers.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 SQTL

:: MORE INFORMATION

Citation

BMC Proc. 2007;1 Suppl 1:S83. Epub 2007 Dec 18.
Semiparametric methods for genome-wide linkage analysis of human gene expression data.
Diao G, Lin DY.

Helium 190903 – Helium Pedigree Visualization Framework

Helium 190903

:: DESCRIPTION

Helium is a generic platform in which various data types can be shown in a pedigree context and we hope to have a beta version available soon that users can download and experiment with.

::DEVELOPER

Information & Computational Sciences, The James Hutton Institute

:: SCREENSHOTS

 Helium

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 Helium

 :: MORE INFORMATION

PRT 2.22 – Pedigree Reconstruction Tools

PRT 2.22

:: DESCRIPTION

PRT (Pedigree Reconstruction Tools) is a software for the reconstruction of single generation sibling groups (SG). A wider range of enumeration algorithms is included, permitting improved computational performance. In particular, an iterative version of the algorithm designed for larger samples is included in a fully automated form.

::DEVELOPER

Anthony Almudevar, PhD

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 PRT

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2012 Jan;12(1):164-78. doi: 10.1111/j.1755-0998.2011.03061.x. Epub 2011 Aug 26.
A new version of PRT software for sibling groups reconstruction with comments regarding several issues in the sibling reconstruction problem.
Almudevar A, Anderson EC.

PEDIBD – Pedigree IBD & Haplotype Inference

PEDIBD

:: DESCRIPTION

PEDIBD infers pairwise Infer identical-by-descent (IBD) and skips haplotype and inheritance construction

::DEVELOPER

Xin Li 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • MatLab

:: DOWNLOAD

  PEDIBD

:: MORE INFORMATION

Citation

J Comput Biol. 2011 Nov;18(11):1411-21. doi: 10.1089/cmb.2011.0167. Epub 2011 Sep 16.
Haplotype reconstruction in large pedigrees with untyped individuals through IBD inference.
Li X1, Li J.

PDT 5.1 – Test for Linkage and Association in General Pedigrees

PDT 5.1

:: DESCRIPTION

The PDT (Pedigree Disequilibrium Test)analysis program allows the user to evaluate evidence of linkage disequilibrium (LD) in general pedigree data. All family data may be used without nullifying the validity of the association test, even when there is more than one affected in a family. The PDT program performs both allele-specific and genotype-specific LD analysis of individual markers. Version 5.1 adds the ability to perform genotype-specific analysis over marker sets.Â

::DEVELOPER

Duke Molecular Physiology Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Unix/Windows

:: DOWNLOAD

PDT

:: MORE INFORMATION

Citation

Eden R. Martin, S. Monks, L. Warren, N. Kaplan (2000)
A Test for Linkage and Association in General Pedigrees:The Pedigree Disequilibrium Test.
Am. J. Hum. Genet. 67:146-154, 2000

SIMLA 3.3 – SIMulation of Pedigree Data for Linkage and Association Studies

SIMLA 3.3

:: DESCRIPTION

SIMLA (SIMulation of pedigree data for Linkage and Association studies) is a SIMulation program that generates data sets of families for use in Linkage and Association studies. It allows the user flexibility in specifying marker and disease placement, locus heterogeneity, disequilibrium between markers and between markers and disease loci. Output is in the form of a LINKAGE pedigree file and is easily utilized, either directly or with minimal reformatting, as input for various genetic analysis packages.

::DEVELOPER

Duke Molecular Physiology Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 SIMLA

:: MORE INFORMATION

Citation

Schmidt MA, Hauser ER, Martin ER, Schmidt S.
Extension of the SIMLA package for gener ating pedigrees with complex inheritance patterns: Environmental covariates, gene-gene and gene-environment interaction.
Stat Appl Genet Mol Biol 4(1): article 15, 2005.