MACOED – Multi-objective Heuristic Optimization Methodology

MACOED

:: DESCRIPTION

MACOED is a multi-objective ant colony optimization algorithm for detecting the genetic interactions.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WIndows/Linux
  • MatLab

:: DOWNLOAD

 MACOED

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Oct 22. pii: btu702.
MACOED: A multi-objective ant colony optimization algorithm for SNP epistasis detection in genome-wide association studies.
Jing PJ, Shen HB

Migrate 4.4.3 – Estimate Population Sizes & Migration Rates

Migrate 4.4.3

:: DESCRIPTION

Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses maximum likelihood or Bayesian inference to jointly estimate all parameters.

It can use the following data types:

  • Sequence data using Felsenstein’s 84 model with or without site rate variation,
  • Single nucleotide polymorphism data (sequence-like data input, HAPMAP-like data input)
  • Microsatellite data using a stepwise mutation model or a brownian motion mutation model (using the repeatlength input format or the fragment-length input format),
  • Electrophoretic data using an ‘infinite’ allele model.

::DEVELOPER

Peter Beerli

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOs / Linux / Unix

:: DOWNLOAD

Migrate-N

:: MORE INFORMATION

Citation

Population Genetic Inference With MIGRATE.
Beerli P, Mashayekhi S, Sadeghi M, Khodaei M, Shaw K.
Curr Protoc Bioinformatics. 2019 Dec;68(1):e87. doi: 10.1002/cpbi.87.

SPEC – Cell Subset Prediction for Blood Genomic Studies

SPEC

:: DESCRIPTION

SPEC is a computational method to predict the cellular source for a pre-defined list of genes (i.e., a gene signature) using gene expression data from total PBMCs

::DEVELOPER

Kleinstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

SPEC

:: MORE INFORMATION

Citation

Bolen CR, Uduman M, Kleinstein SH.
Cell subset prediction for blood genomic studies.
BMC Bioinformatics. 2011 Jun 24;12:258.

mendel-gpu – GPU enabled Haplotying and Genotype Imputation

mendel-gpu

:: DESCRIPTION

mendel-gpu uses OpenCL kernels to rapidly impute genotypes using linkage disequilibrium patterns in unrelated subjects. It is appropriate for resequencing data.

::DEVELOPER

Gary K. Chen, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

  mendel-gpu

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2979-80. doi: 10.1093/bioinformatics/bts536. Epub 2012 Sep 5.
Mendel-GPU: haplotyping and genotype imputation on graphics processing units.
Chen GK1, Wang K, Stram AH, Sobel EM, Lange K.

StructHDP 1.1 – Inference of number of Clusters and Population Structure from Admixed Genotype data.

StructHDP 1.1

:: DESCRIPTION

StructHDP is a program for automatically inferring the population structure and number of clusters from a sample of admixed genotype data. It extends the model used by Structure to allow for a potentially infinite number of populations and then chooses the number of populations that best explain the data.

::DEVELOPER

Suyash Shringarpure

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 StructHDP

:: MORE INFORMATION

Citation

StructHDP: automatic inference of number of clusters and population structure from admixed genotype data Suyash Shringarpure;
Suyash Shringarpure ,Daegun Won; Eric P. Xing
Bioinformatics 2011 27: i324-i332

Chimera – Exploiting Hidden Information Interleaved in the Redundancy of the Genetic Code

Chimera

:: DESCRIPTION

Chimera is an unsupervised computationally efficient approach for exploiting hidden high dimensional information related to the way gene expression is encoded in the ORF, based solely on the genome of the analysed organism.

::DEVELOPER

Tamir Tuller’s Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 Chimera

:: MORE INFORMATION

Citation

Exploiting Hidden Information Interleaved in the Redundancy of the Genetic Code without Prior Knowledge.
Zur H, Tuller T.
Bioinformatics. 2014 Nov 29. pii: btu797.

SeqPop – Compute Population Genetics Statistics on Sequence Data

SeqPop

:: DESCRIPTION

SeqPop is a program for computing population genetics statistics on sequence data, including Pn, Theta, Pi(i,j), Kst(*), Fst(*), and their Monte Carlo significance for population subdivision.

::DEVELOPER

the Townsend Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac

:: DOWNLOAD

  SeqPop

:: MORE INFORMATION

traitRate 201612 – Detection of Trait-dependent Shifts in the Rate of Sequence Evolution

traitRate 201612

:: DESCRIPTION

traitRate is a program for the detection of trait-dependent shifts in the rate of sequence evolution.

::DEVELOPER

Mayrose Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

  traitRate

:: MORE INFORMATION

Citation

Mayrose I and Otto SP. 2011.
A Likelihood Method for Detecting Trait-Dependent Shifts in the Rate of Molecular Evolution.
Mol Biol Evol. 28:781-791.

Clumpak 20150326 – Model-based Population Structure Analysis

Clumpak 20150326

:: DESCRIPTION

Clumpak (Cluster Markov Packager Across K) is a method that automates the postprocessing of results of model-based population structure analyses.

::DEVELOPER

Mayrose Lab, Tel Aviv University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX
  • Perl

:: DOWNLOAD

 Clumpak

:: MORE INFORMATION

Citation:

Mol Ecol Resour. 2015 Feb 12. doi: 10.1111/1755-0998.12387.
Clumpak: a program for identifying clustering modes and packaging population structure inferences across K.
Kopelman NM1, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I.