Baypass 2.1 – Genome-Wide Scan for Adaptive Differentiation and Association Analysis with Population-specific Covariables

Baypass 2.1

:: 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.

pong – Fast Analysis and Visualization of Latent Clusters in Population Genetic data

pong

:: DESCRIPTION

pong is a freely available software package for post-processing output from clustering inference using population genetic data

::DEVELOPER

the Ramachandran Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • Python

:: DOWNLOAD

 pong

:: MORE INFORMATION

Citation

pong: fast analysis and visualization of latent clusters in population genetic data.
Behr AA, Liu KZ, Liu-Fang G, Nakka P, Ramachandran S.
Bioinformatics. 2016 Jun 9. pii: btw327.

ACG – Inference of Population History from Genetic data

ACG

:: DESCRIPTION

ACG (Ancestral Recombination Graph) is a graphical desktop application that allows genetics researchers to infer properties of a population based on genetic sequences sampled from it.

::DEVELOPER

Brendan O’Fallon (brendan.d.ofallon@aruplab.com).

:: SCREENSHOTS

ACG

:: REQUIREMENTS

  • Linux /Windows / MacOsX
  • Java

:: DOWNLOAD

 ACG

:: MORE INFORMATION

Citation:

ACG: rapid inference of population history from recombining nucleotide sequences.
O’Fallon BD.
BMC Bioinformatics. 2013 Feb 5;14:40. doi: 10.1186/1471-2105-14-40.

TreesimJ 0.7 – Population Genetics Simulator Program

TreesimJ 0.7

:: DESCRIPTION

TreesimJ is a flexible, individual-based population genetic simulator. It tracks the state of a population evolving in forward time via discrete, Wright-Fisher generations.   It also maintains the full genealogical tree of the population and allows for collecting sample trees which can be analyzed, exported and logged.  It can also simulate evolving DNA under a variety of assumptions regarding mutation and selection. TreesimJ is very flexible, meaning that a wide variety of fitness models, demographic models, and data collectors are supported, and new models are easy to write.  The application also sports an intuitive graphical interface, so users unfamiliar with the command line or XML can easily use the program to generate and analyze genetic data.

::DEVELOPER

Brendan O’Fallon

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

TreesimJ

:: MORE INFORMATION

Citation:

Brendan O’Fallon
TreesimJ: a flexible, forward time population genetic simulator
Bioinformatics (2010) 26 (17): 2200-2201

FastEPRR 1.0 – Fast Estimation of Population Recombination Rates

FastEPRR 1.0

:: DESCRIPTION

FastEPRR is an extremely fast open-source software package to estimate population recombination rate based on intraspecific DNA polymorphism data.

::DEVELOPER

Evolutionary Genomics Lab, PICB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 FastEPRR

:: MORE INFORMATION

Citation

New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era.
Gao F, Ming C, Hu W, Li H.
G3 (Bethesda). 2016 Mar 30. pii: g3.116.028233. doi: 10.1534/g3.116.028233

ScaffoldSeq – Characterization of Directed Evolution Populations

ScaffoldSeq

:: DESCRIPTION

ScaffoldSeq is software designed for the numerous applications – including directed evolution analysis – in which a user generates a population of DNA sequences encoding for partially diverse proteins with related functions and would like to characterize the single site and pairwise amino acid frequencies across the population.

::DEVELOPER

Hackel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Python

:: DOWNLOAD

 ScaffoldSeq

:: MORE INFORMATION

Citation

ScaffoldSeq: Software for characterization of directed evolution populations.
Woldring DR, Holec PV, Hackel BJ.
Proteins. 2016 Mar 28. doi: 10.1002/prot.25040.

flowCL 1.8.0 – Semantic labelling of Flow Cytometric Cell Populations

flowCL 1.8.0

:: DESCRIPTION

flowCL is a software package that performs semantic labelling of cell populations based on their surface markers and applied it to labelling of the Federation of Clinical Immunology Societies Human Immunology Project Consortium lyoplate populations as a use case.

::DEVELOPER

Justin Meskas <jmeskas at bccrc.ca>, Radina Droumeva

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

 flowCL

:: MORE INFORMATION

Citation

flowCL: ontology-based cell population labelling in flow cytometry.
Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Renani JT, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR.
Bioinformatics. 2014 Dec 6. pii: btu807.

SimRA – Simulates Generic Multiple Population Evolution Model with Admixture

SimRA

:: DESCRIPTION

SimRA (Simulation based on Random-graphs Algorithms) is a framework for simulating generic and complex evolutionary scenarios of multiple populations with subdivision and admixture.

::DEVELOPER

IBM Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • JRE

:: DOWNLOAD

 SimRA

:: MORE INFORMATION

Citation

Sampling ARG of multiple populations under complex configurations of subdivision and admixture.
Carrieri AP, Utro F, Parida L.
Bioinformatics. 2015 Dec 7. pii: btv716.

TEMP v1.04 – Analyzing Transposable Element Polymorphism in Populations

TEMP v1.04

:: DESCRIPTION

TEMP is a software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data

::DEVELOPER

Jiali Zhuang (jiali.zhuang@umassmed.edu) and Jie Wang (jie.wangj@umassmed.edu) @ ZLab, University of Massachusetts Medical School, Worcester, MA, USA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TEMP

:: MORE INFORMATION

Citation

TEMP: a computational method for analyzing transposable element polymorphism in populations.
Zhuang J, Wang J, Theurkauf W, Weng Z.
Nucleic Acids Res. 2014 Jun;42(11):6826-38. doi: 10.1093/nar/gku323.

Genepop 4.5 – Population Genetics Software Package

Genepop 4.5

:: DESCRIPTION

GENEPOP is a population genetics software package

::DEVELOPER

Michel Raymond (Raymond@isem.univ-montp2.fr) and Francois Rousset (Rousset@isem.univ-montp2.fr)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux  / Windows

:: DOWNLOAD

 Genepop

:: MORE INFORMATION

Citation

Rousset, F., 2008.
Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux.
Mol. Ecol. Resources 8: 103-106.