SPADS 1.0 – Spatial and Population Analysis of DNA Sequences

SPADS 1.0

:: DESCRIPTION

SPADS is a population genetics software computing several summary statistics from populations or groups of populations, and implementing two clustering algorithms to study the genetic structure of populations. SPADS has been specifically developed for the analysis of DNA sequences. The first aim of SPADS is to compute, on real datasets, the summary statistics computed by PhyloGeoSim on each simulated datasets.

::DEVELOPER

Evolutionary Biology & Ecology, Université Libre de Bruxelles

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 SPADS

:: MORE INFORMATION

Citation

SPADS 1.0: a toolbox to perform spatial analyses on DNA sequence datasets.
Dellicour S, Mardulyn P.
Mol Ecol Resour. 2013 Nov 11. doi: 10.1111/1755-0998.12200

SMETHILLIUM 1.2 – Spatial normalisation METHod for ILLumina InfinIUM HumanMethylation BeadChip

SMETHILLIUM 1.2

:: DESCRIPTION

SMETHILLIUM is a  spatial normalisation method for ILLumina InfinIUM HumanMethylation BeadChip. DNA methylation is a major epigenetic modification in human cells. Illumina HumanMethylation27 BeadChip investigates the methylation of 27,578 loci in the genome. We developed a normalisation method to correct the spatial background noise which affect the signal-to-noise ratio. The prediction performance of the proposed method was assessed on methylated and unmethylated samples. We demonstrate that the spatial normalisation outperforms BeadStudio to predict the methylation status of a given locus

::DEVELOPER

Computational Systems Biology of Cancer group in Bioinformatics Laboratory of Institut Curie (Paris).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  SMETHILLIUM

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Jun 15;27(12):1693-5. Epub 2011 Apr 14.
SMETHILLIUM: spatial normalization method for Illumina infinium HumanMethylation BeadChip.
Sabbah C, Mazo G, Paccard C, Reyal F, Hupé P.

SPA 1.13 – Spatial Ancestry Analysis in Genetic data

SPA 1.13

:: DESCRIPTION

SPA is a method for predicting ancestry or where an individual is from using the individual’s DNA. Accurately modeling ancestry is an important step in identifying genetic variation involved in disease.

::DEVELOPER

ZarLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 SPA

:: MORE INFORMATION

Citation

Wen-Yun Yang, John Novembre, Eleazar Eskin and Eran Halperin.
A model based approach for analysis of spatial structure in genetic data.
Nature Genetics, 44, 725–731 (2012).

Spatial 1.0.0 – Model Animal Movement on Landscapes

Spatial 1.0.0

:: DESCRIPTION

Spatial is an agent-based model of the movements of animals on landscapes. The landscapes can be entered from image files or from tables of data. Rules are entered to describe the attractiveness, permeability, and rate of movement of animals for each landscape feature (optionally including other animals). Spatial then simulates the movements over time, and dsiplays final location, tracks, or density of occupancy.

::DEVELOPER

The SCTI Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Spatial 

:: MORE INFORMATION