Tag: Populations

Saguaro 0.1 – Detect Signatures of Selection within Populations, Strains, or Species

Saguaro 0.1

:: DESCRIPTION

Saguaro (Genome-Wide) , SaguaroGW,is a program to detect signatures of selection within populations, strains, or species. It takes SNPs or nucleotides as input, and creates statistical local phylogenies for each region in the genome.

::DEVELOPER

the Science for Life Laboratory, Uppsala University, and the Broad Institute of MIT and Harvard.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Saguaro

:: MORE INFORMATION

Citation:

BMC Genomics. 2013 May 24;14:347. doi: 10.1186/1471-2164-14-347.
Unsupervised genome-wide recognition of local relationship patterns.
Zamani N1, Russell P, Lantz H, Hoeppner MP, Meadows JR, Vijay N, Mauceli E, di Palma F, Lindblad-Toh K, Jern P, Grabherr MG.

FFPopSim 2.0 – Forward Simulation package for the Evolution of large Populations

FFPopSim 2.0

:: DESCRIPTION

FFPopSim (Fast Forward Population Genetic Simulation) is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the product of mutation rate and population size is larger than one. It consists of one library for individual-based simulations, and a complementary one for simulation of the entire genotype distribution.

::DEVELOPER

FFPopSim team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • C++ Compiler
  • Python

:: DOWNLOAD

 FFPopSim

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Dec 15;28(24):3332-3. doi: 10.1093/bioinformatics/bts633. Epub 2012 Oct 24.
FFPopSim: an efficient forward simulation package for the evolution of large populations.
Zanini F, Neher RA.

BWBBLE – Short Read Alignment with Populations of Genomes

BWBBLE

:: DESCRIPTION

BWBBLE performs short-read alignment to a population of genomes represented by a reference multi-genome.

::DEVELOPER

Serafim’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • C Compiler

:: DOWNLOAD

 BWBBLE

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):i361-70. doi: 10.1093/bioinformatics/btt215.
Short read alignment with populations of genomes.
Huang L, Popic V, Batzoglou S.

AlphaImpute 1.9.8.3 – Imputing and Phasing Genotype data in Populations

AlphaImpute 1.9.8.3

:: DESCRIPTION

AlphaImpute is a software package for imputing and phasing genotype data in populations with pedigree information. AlphaImpute combines long range phasing with segregation analysis and haplotype library imputation (SAHLI) methodology to impute alleles and genotypes.

::DEVELOPER

AlphaGenes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 AlphaImpute

:: MORE INFORMATION

Citation

Genet Sel Evol. 2013 Apr 25;45:10. doi: 10.1186/1297-9686-45-10.
Extending long-range phasing and haplotype library imputation methods to impute genotypes on sex chromosomes.
Hickey JM1, Kranis A.

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