GitHub - txje/compatible-intervals: Methods for computing genome-wide four-gamete compatible intervals describing local phylogenetic structure

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Methods for computing genome-wide four-gamete compatible intervals describing local phylogenetic structure

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Name		Name	Last commit message	Last commit date
Latest commit History 5 Commits
example		example
LICENSE		LICENSE
README		README
__init__.py		__init__.py
compatibility_matrix.py		compatibility_matrix.py
compute_intervals.py		compute_intervals.py
genotype_intervals.py		genotype_intervals.py
haplotype_character_removal_intervals.py		haplotype_character_removal_intervals.py
hapmap.py		hapmap.py
maxk.py		maxk.py
mpdag.py		mpdag.py
mvc.py		mvc.py
simple_haplotype_intervals.py		simple_haplotype_intervals.py
util.py		util.py

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Copyright (c) 2008-2014 Jeremy Wang
Available under an MIT License (see LICENSE)

Compatible Intervals

My thesis describes this work:
Analysis and Visualization of Local Phylogenetic Structure within Species (Jeremy Wang, UNC-Chapel Hill, 2013)

J. Wang, K. Moore, Q. Zhang, F. Villena, W. Wang, and L. McMillan. Genome-wide
compatible SNP intervals and their properties. Proceedings of ACM International
Conference on Bioinformatics and Computational Biology, 2010.

There are three conceptually distinct methods:
1. Compatible intervals using homozygous genotype data (simple_haplotype_intervals.py)
2. Compatible intervals using heterozygous genotype data (genotype_intervals.py)
3. Compatible intervals allowing character removal (error-resistant) using homozygous genotype data (haplotype_character_removal_intervals.py)

There also exists a module for rendering compatibility matrix figures (compatibility_matrix.py)

mpdag.py and mvc.py are helper modules to perform various graph operations
util.py contains anything else