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SheepTreeSeq: Scalable analysis of sheep genome diversity using tree sequences

Setting up the environment

Project Setup
Build the documentation

Introducing TreeSequences

Quickstart
Getting started with tskit
TSINFER tutorial
TSINFER with SMARTER test data
Inference from a test VCF file

Simulating TreeSequences

Analyze the simulated data
Test TreeSequences with different mutation rates
Dataset for TS inference
Explore threads metadata
Threads fitting data

The SMARTER database

The SMARTER-database
Get SMARTER samples list
Infer ancestry using EST-SFS
Reading data from chromosome 26
Nucleotide diversity
About tstree space
Get ancient information from ensemble compara
SMARTER 50K
50K simulations results
Population statistics
Population statistics plots

Repository
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By Paolo Cozzi

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