Tag: Population

SIMCOAL 2.1.2 – Simulation of Molecular data in interconnected Populations with Arbitrary Demography

SIMCOAL 2.1.2

:: DESCRIPTION

SIMCOAL (SIMulate COAlescence) is a computer program for the simulation of molecular genetic diversity in an arbitrary number of haploid populations examined for a set of fully linked loci.

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 SIMCOAL

:: MORE INFORMATION

Citation

Excoffier, Novembre, Schneider (2000),
“SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography“,
Journal of Heredity, 91:506-509.

SAMOVA 2.0 – Define the Genetic Structure of Population

SAMOVA 2.0

:: DESCRIPTION

SAMOVA (Spatial Analysis of MOlecular VAriance) implements an approach to define groups of populations that are geographically homogeneous and maximally differentiated from each other. As a by-product, it also leads to the identification of genetic barriers between these groups. The method is based on a simulated annealing procedure that aims at maximizing the proportion of total genetic variance due to differences between groups of populations

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SAMOVA

:: MORE INFORMATION

Citation

Dupanloup, I, S. Schneider, L. Excoffier (2002)
A simulated annealing approach to define the genetic structure of populations.
Molecular Ecology 11: 2571-81.

AlphaSeqOpt – Determining Optimum Distribution of Sequencing Resources within Population of interest

AlphaSeqOpt

:: DESCRIPTION

AlphaSeqOpt is a software package for determining the optimum distribution of sequencing resources within a population of interest. AlphaSeqOpt determines which individuals should be prioritised for sequencing and the total investment to be made in sequencing this individual. The aim of the algorithm is to capture, sequence and phase as many of the population haplotypes as possible for maximum sequence imputation ability into the rest of the population.

::DEVELOPER

AlphaGenes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows

:: DOWNLOAD

AlphaSeqOpt

:: MORE INFORMATION

Citation

Ros-Freixedes R, Gonen S, Gorjanc G, Hickey JM.
A method for allocating low-coverage sequencing resources by targeting haplotypes rather than individuals.
Genet Sel Evol. 2017 Oct 25;49(1):78. doi: 10.1186/s12711-017-0353-y. PMID: 29070022; PMCID: PMC5655873.

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.

ALCHEMY 1.07 – An automated, Population Genetic model driven SNP Genotype Calling method

ALCHEMY 1.07

:: DESCRIPTION

ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods.

::DEVELOPER

ALCHEMY team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 ALCHEMY 

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Dec 1;26(23):2952-60. doi: 10.1093/bioinformatics/btq533. Epub 2010 Oct 5.
ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations.
Wright MH1, Tung CW, Zhao K, Reynolds A, McCouch SR, Bustamante CD.

BioBin 2.3.0 – Explore Rare Variant Population Stratification

BioBin 2.3.0

:: DESCRIPTION

BioBin meets a critical need for an improved binning algorithm through the advantage of prior biological knowledge and potential cumulative effects of biologically aggregated RVs. BioBin requires the Library of Knowledge Integration (LOKI), which contains diverse prior knowledge from multiple collections of biological data. BioBin can be used to apply multiple levels of burden collapsing/testing, including: regulatory regions, evolutionary conserved regions, genes, and/or pathways without a need for an external feature file. BioBin aids rare variant analysis by binning variants according to prior biological knowledge.

::DEVELOPER

Ritchie Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 BioBin

:: MORE INFORMATION

Citation

Pac Symp Biocomput. 2013:332-43.
Using BioBin to explore rare variant population stratification.
Moore CB, Wallace JR, Frase AT, Pendergrass SA, Ritchie MD.

PSAT – Population Stratification Association Test

PSAT

:: DESCRIPTION

PSAT (Population Stratification Association Test) is a software for testing association between single nucleotide polymorphisms (SNPs) and a disease with stratification. Population stratification can be a serious obstacle in the analysis of genome-wide association studies. We have developed a method for evaluating the significance of association scores in whole-genome cohorts with stratification. Our approach is a randomization test akin to a standard permutation test. It conditions on the genotype matrix and thus takes account not only of the population structure but also of the complex linkage disequilibrium structure of the genome. As we show in simulation experiments, our method achieves higher power and significantly better control over false positive rates than existing methods. In addition, it can be easily applied to whole genome association studies.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows with Cygwin /Linux

:: DOWNLOAD

  PSAT

:: MORE INFORMATION

Citation

A randomization test for controlling population stratification in whole-genome association studies
G. Kimmel, M.I. Jordan, E. Halperin, R. Shamir and R.M. Karp RM
American Journal of Human Genetics (2007) , Vol. 81 No. 5, 895-905 (2007)

Baypass 2.2 – Genome-Wide Scan for Adaptive Differentiation and Association Analysis with Population-specific Covariables

Baypass 2.2

:: DESCRIPTION

The package BayPass is a population genomics software which is primarily aimed at identifying genetic markers subjected to selection and/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics).

::DEVELOPER

Centre de Biologie et Gestion des Populations (CBGP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Baypass

:: MORE INFORMATION

Citation

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates.
Gautier M.
Genetics. 2015 Dec;201(4):1555-79. doi: 10.1534/genetics.115.181453.

SimulaTE 1.13 – Simulating Complex Landscapes of Transposable Elements of Populations

SimulaTE 1.13

:: DESCRIPTION

SimulaTE allows to simulate arbitrary complex landscapes of transposable elements (TEs). Additionally reads may be simulated using the genomes of all indivdiuals in the population as template. Reads may be simulated using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). SimulaTE will greatly aid in evaluating the suitability of different approaches for estimating TE abundance within populations and to test whether given genomic resources, such as a reference genome or a TE database (a fasta file containing consensus sequences of TEs), are suitable for TE identification.

::DEVELOPER

Institute of Population Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

SimulaTE

:: MORE INFORMATION

Citation:

SimulaTE: simulating complex landscapes of transposable elements of populations.
Kofler R.
Bioinformatics. 2018 Apr 15;34(8):1419-1420. doi: 10.1093/bioinformatics/btx772.