LICENSE.txt
MANIFEST.in
README.md
classifiers.txt
requirements.txt
setup.cfg
setup.py
pydigree/__init__.py
pydigree/common.py
pydigree/exceptions.py
pydigree/ibs.py
pydigree/individual.py
pydigree/individualcontainer.py
pydigree/paths.py
pydigree/pedigree.py
pydigree/pedigreecollection.py
pydigree/phenotypes.py
pydigree/population.py
pydigree/rand.py
pydigree/recombination.py
pydigree.egg-info/PKG-INFO
pydigree.egg-info/SOURCES.txt
pydigree.egg-info/dependency_links.txt
pydigree.egg-info/top_level.txt
pydigree/cydigree/__init__.py
pydigree/cydigree/cyfuncs.c
pydigree/cydigree/cyfuncs.pyx
pydigree/cydigree/datastructures.c
pydigree/cydigree/datastructures.pyx
pydigree/cydigree/sparray2.c
pydigree/cydigree/sparray2.cpp
pydigree/cydigree/sparsearray.cpp
pydigree/cydigree/sparsearray.pyx
pydigree/cydigree/sparsearray2.cpp
pydigree/cydigree/varianttree.c
pydigree/cydigree/vcfparse.c
pydigree/cydigree/vcfparse.pyx
pydigree/datastructures/__init__.py
pydigree/genotypes/__init__.py
pydigree/genotypes/alleles.py
pydigree/genotypes/chromosometemplate.py
pydigree/genotypes/genoabc.py
pydigree/genotypes/genotypecontainers.py
pydigree/genotypes/labelledalleles.py
pydigree/genotypes/sparsealleles.py
pydigree/io/__init__.py
pydigree/io/base.py
pydigree/io/beagle.py
pydigree/io/genomesimla.py
pydigree/io/kinship.py
pydigree/io/plink.py
pydigree/io/sgs.py
pydigree/io/smartopen.py
pydigree/io/vcf.py
pydigree/sgs/__init__.py
pydigree/sgs/sgs.py
pydigree/simulation/__init__.py
pydigree/simulation/chromosomepool.py
pydigree/simulation/mating.py
pydigree/simulation/trait.py
pydigree/simulation/genedrop/__init__.py
pydigree/simulation/genedrop/constrained_mendelian.py
pydigree/simulation/genedrop/naivegenedrop.py
pydigree/simulation/genedrop/simulation.py
pydigree/stats/__init__.py
pydigree/stats/mathfuncs.py
pydigree/stats/stattests.py
pydigree/stats/variancecomponents.py
pydigree/stats/mixedmodel/__init__.py
pydigree/stats/mixedmodel/likelihood.py
pydigree/stats/mixedmodel/maximization.py
pydigree/stats/mixedmodel/mixedmodel.py
pydigree/stats/mixedmodel/mixin.py
sample_pedigrees/charlesii.ped
sample_pedigrees/double_first_cousins.ped
sample_pedigrees/first_cousin_child.ped
sample_pedigrees/first_cousins.ped
sample_pedigrees/fullsib.ped
sample_pedigrees/half_sibs.ped
sample_pedigrees/repeated_fullsib_mating.ped
sample_pedigrees/simultaneous_cousin_sib.ped
sample_pedigrees/tunisia_autosomal_recessive_ataxia.ped
sample_pedigrees/vz_huntington_autosomal_dominant.ped
scripts/.DS_Store
scripts/bitsize.py
scripts/bitsize.py.bak
scripts/frequencies.py
scripts/frequencies.py.bak
scripts/genedrop.py
scripts/genedrop.py.bak
scripts/genedrop.py.lprof
scripts/kinship.py
scripts/kinship.py.bak
scripts/polygenic.py
scripts/polygenic.py.bak
scripts/sim_pool.py
scripts/sim_pool.py.bak
scripts/sim_pool.py.lprof
scripts/sim_pool.py~
scripts/sim_population.py
scripts/sim_population.py.bak
scripts/simcohort.py
scripts/simcohort.py.bak
scripts/simulate_pedigree_data.py
scripts/simulate_pedigree_data.py.bak
scripts/vc_assoc.py
scripts/vc_assoc.py.bak
support/.DS_Store
support/affecteds_ibd_from_founder.py
support/affecteds_ibd_from_founder.py.bak
support/autodom.sh
support/cyprofile.py
support/cyprofile.py.bak
support/makepxd.py
support/mean_genotypic_value.py
support/mean_genotypic_value.py.bak
support/null.sh
support/randchrom.chrom
support/randchrom.chrom~
support/random_chromosome.py~
support/recombiner.py
support/recombiner.py.bak
support/t.py~
support/test_segments.py
support/test_segments.py.bak