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BayesAss+ estiamtion of populations migrat... (1)

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BayesAss+ is a program that estimates recent migration rates between populations using MCMC. It also estimates each individual’s immigrant ancestry, the generation in which immigration occurred (i.e. the individual can be assigned as an immigrant from a specific population, a non-immigrant, or the offspring of an immigrant and a non-immigrant), the population (as opposed to the sample) allele frequencies, inbreeding (F) values within each population, and genotypes at any locus wit...

Created: 2012-03-08

Credits: Pipeline

Fdist2 Simulation Pipeline Workflow (1)

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Fdist2 is a simulation program to detect loci that might be under selection in samples from structured populations.   Workflow Usage & Specifications The workflow reads an input file "fdist_params2.dat", which consists of 6 lines. This file must only contain numbers in the format described: Total number of demes (100 max). No of populations sampled (must be less than or equal to total number of demes). Expected Fst for infinite allele, infinite island model. Sample si...

Created: 2012-03-08 | Last updated: 2012-03-08

Credits: Pipeline

Migrate Pipeline Workflow (1)

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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.     Workflow Usage & Specifications Migrate can use the following data types: •Sequence data using Felsenstein's 84 model with or without site rate variation, •Single nucleotide poly...

Created: 2012-03-08

Credits: Pipeline

BLAST (1)

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This is a simple workflow demonstrating a sequence Basic Local Alignment Search Tool (BLAST).                                                                                           

Created: 2012-01-26 | Last updated: 2012-01-26

Credits: Pipeline

Deformable Organisms Skullstripping (1)

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Overview - Deformable Organisms Skullstripping Pipeline will skull-strip an magnetic resonance (MR) image of the brain using a deformable organisms framework. Problem addressed by this workflow Segment or delineate the brain in whole head MR images. Creates a mask of the brain, separating it from skull, skin, eyes, neck, and cerebro-spinal fluid (CSF). Detailed Workflow Usage & Specifications The module takes ANALYZE or NIFTI magnetic resonance images of the head as input a...

Created: 2011-09-14

Credits: Azamanyan

BATWING (1)

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Batwing reads in multi-locus haplotype data, and model and prior distri- bution specifications, and uses a Markov chain Monte Carlo (MCMC) method based on coalescent theory to generate approximate random samples from the posterior distributions of parameters such as mutation rates, effective population sizes and growth rates, and times of population splitting events. It also generates approximate posterior samples of the entire genealogical tree underly- ing the sample, including the tree hei...

Created: 2011-08-25 | Last updated: 2011-08-25

Credits: Pipeline

Mouse Brain Image Analysis: General Linear... (1)

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Overview - General Linear Model The workflow runs voxelwise statistics on two populations of mice. Each of the populations has been scanned prior to injection of a label and at four subsequent timepoints.   Problem addressed by this workflow The workflow addresses several problems. First of all, it performs co-registration between the subjects from the two populations and at different timepoints. It then scales all images. Finally, it runs a multiple linear regression module t...

Created: 2011-04-06 | Last updated: 2011-04-06

Credits: Pipeline

Automated BrainSuite Cortical Surface Extr... (1)

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Overview - BrainSuite Cortical Surface Extraction The workflow takes a skull stripped volume as input and runs a multi-stage process, extracting the cortical surface and splitting it into hemispheres.   Problem addressed by this workflow Generating a shape model of the cortical surface from a 3D volume.   Detailed Workflow Usage & Specifications Tissue Classification The next step in the Brainsuite09 cortical surface identification sequence is tissue classificatio...

Created: 2011-04-06 | Last updated: 2011-04-06

Credits: Pipeline

First Level within subject fMRI processing (1)

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Overview - fMRI-FEAT workflow This is a simple with-in subject fMRI analysis workflow. It takes 3D fMRI images and structural images of a subject and performs FSLmerge, BET (if the data is not already skull stripped) and first level FEAT processing.   Problem addressed by this workflow FSLMerge, BET and FEAT first level analysis can be performed using this workflow on one or more subjects that require the same processing. The design FSF file is generate using the FSL FEAT inte...

Created: 2011-04-06 | Last updated: 2011-07-14

Credits: Pipeline

Image Registration Meta Algorithm (IRMA) (1)

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Overview - Workflow-Title In this workflow different registration algorithms are applied to the same image and the image that is best registered to the template is chosen as the output top candidate.   Problem addressed by this workflow In this workflow various registration algorithm is performed on the same subject. The algorithm that gives the best result is chosen. This might be different for different input images. This workflow is robust and picks the best-registered imag...

Created: 2011-04-06 | Last updated: 2011-07-14

Credits: Pipeline