GENOMEPOP 2.7.7.1 – Evolve Populations of Genomes under complex Evolution Models and Demography

GENOMEPOP 2.7.7.1

:: DESCRIPTION

Genomepop is flexible software that allows the forward simulation of DNA sequences in a metapopulation context under a variety of conditions. Users can input their own sequences or tell the program to generate them. Retro and recurrent mutation can be allowed or neglected. A number of populations with any migration model can be defined. Each population consists of a number N of sequences or genomes.

::DEVELOPER

Antonio Carvajal-Rodriguez

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

GENOMEPOP

:: MORE INFORMATION

Citation

Antonio Carvajal-Rodriguez (2008)
GENOMEPOP: A program to simulate genomes in populations
BMC Bioinformatics 9: 223

Reveel 201610 – Large-scale Population Genotyper using low-coverage Sequencing data

Reveel 201610

:: DESCRIPTION

Reveel is an ultrafast tool for single nucleotide variant calling and genotyping of large cohorts that have been sequenced at low coverage.

::DEVELOPER

Serafim’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Java

:: DOWNLOAD

Reveel

:: MORE INFORMATION

Citation

Reveel: large-scale population genotyping using low-coverage sequencing data.
Huang L, Wang B, Chen R, Bercovici S, Batzoglou S.
Bioinformatics. 2015 Sep 9. pii: btv530.

EIGENSOFT 7.2.1 – Population Structure , Eigenanalysis & Stratification

EIGENSOFT 7.2.1

:: DESCRIPTION

EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.

::DEVELOPER

Reich laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

EIGENSOFT

:: MORE INFORMATION

Citation:

Nature Genetics 38, 904 – 909 (2006) Published online: 23 July 2006; | doi:10.1038/ng1847
Principal components analysis corrects for stratification in genome-wide association studies
Alkes L Price, Nick J Patterson, Robert M Plenge, Michael E Weinblatt, Nancy A Shadick & David Reich

Population Structure and Eigenanalysis
Nick Patterson, Alkes L. Price, David Reich
December 2006 Issue of PLoS Genetics

Genetix 4.05 – Set of Population Genetics Programs

Genetix 4.05

:: DESCRIPTION

Genetix is a set of programs which computes several basic parameters of population genetics such as Nei’s D and H, Wright’s F-statistics (the Weir-Cockerham’s and Robertson-Hill’s estimators), and linkage disequilibrium D according to Black & Krafsur. For each of them, the distribution of the parameter values under the null hypothesis (for instance Hardy-Weinberg equilibrium for Fstats) is generated by the appropriate resampling scheme of the relevant objects (e.g. alleles between individuals in the case of Fis) using permutations.

::DEVELOPER

Genetix team

:: SCREENSHOTS

::REQUIREMENTS

Windows

:: DOWNLOAD

Genetix

:: MORE INFORMATION

PopIns 1.0.1 – Population-scale Detection of Novel Sequence Insertions

PopIns 1.0.1

:: DESCRIPTION

PopIns can discover and characterize non-reference insertions of 100 bp or longer on a population scale.

::DEVELOPER

PopIns team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
SeqAn
bwa
velvet
samtools
sickle

:: DOWNLOAD

PopIns

:: MORE INFORMATION

Citation:

PopIns: population-scale detection of novel sequence insertions.
Kehr B, Melsted P, Halldórsson BV.
Bioinformatics. 2015 Apr 28. pii: btv273.

popRange – A Spatially & Temporally Explicit Forward Population Genetic Simulator

popRange 1.1.3

:: DESCRIPTION

popRange is a forward genetic simulator, which incorporates large-scale genetic data with stochastic spatially and temporally explicit demographic and selective models.

::DEVELOPER

Kimberly McManus

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux/ MacOsX
R
Python

:: DOWNLOAD

popRange

:: MORE INFORMATION

Citation

Source Code Biol Med. 2015 Apr 11;10:6. doi: 10.1186/s13029-015-0036-4. eCollection 2015.
popRange: a highly flexible spatially and temporally explicit Wright-Fisher simulator.
McManus KF

Outbreak 2.11.0 – Predict Survival of Reintroduced Populations

Outbreak 2.11.0

:: DESCRIPTION

Outbreak simulates disease dynamics under an individually base model of transitions among susceptible, exposed, infectious and recovered individuals. Outbreak provides several options for modes of transmission (random contact within populations, spatially based transmission, contact with environmental sources of disease) and provides options for management through vaccination or culling.

::DEVELOPER

The SCTI Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

Outbreak

:: MORE INFORMATION

Vortex 10.5.5 – Population Viability Analysis software

Vortex 10.5.5

:: DESCRIPTION

Vortex is an individual-based simulation of deterministic forces as well as demographic, environmental and genetic stochastic events on wildlife populations. It can model many of the extinction vortices that can threaten persistence of small populations.

::DEVELOPER

The SCTI Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

Vortex

:: MORE INFORMATION

Citation

Lacy, R.C. 2000.
Structure of the VORTEX simulation model for population viability analysis.
Ecological Bulletins 48:191-203.

RedLynx v1.1 – Population Genetics Simulator

RedLynx v1.1

:: DESCRIPTION

RedLynx is a population genetics simulator built entirely in JavaScript. It runs entirely withing a web browser and is extremely helpful when teaching population genetics and evolution. It can simulate genetic drift, selection, dominance, mutation, and migration.

::DEVELOPER

Reed A. Cartwright

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

LDlink / LDlinkR 1.1.2 – Linkage Disequilibrium in Population group

LDlink / LDlinkR 1.1.2

:: DESCRIPTION

LDlink is a suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups.

LDhap: Calculate population specific haplotype frequencies of all haplotypes observed for a list of query SNPs. Input is a list of SNP RS numbers (one per line) and a population group.

LDmatrix: Create an interactive heatmap matrix of pairwise linkage disequilibrium statistics. Input is a list of SNP RS numbers (one per line) and a population group.

LDpair: Investigate correlated alleles for a pair of SNPs in high LD. Input is two RS numbers and a population group.

LDproxy: Interactively explore proxy and putatively functional SNPs for a query SNP. Input is an RS number and a population group.

::DEVELOPER

Mitchell Machiela in collaboration with NCI’s Center for Biomedical Informatics and Information Technology (CBIIT).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser
R

:: DOWNLOAD

LDlinkR

:: MORE INFORMATION

Citation

LDlink: A web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants.
Machiela MJ, Chanock SJ.
Bioinformatics. 2015 Jul 2. pii: btv402.