/
__init__.py
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/
__init__.py
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#!/usr/bin/env python
# version is the same as ipyrad
from ipyrad import __version__
# analysis tools will have a class object that is upper case, which is
# called by a convenience function which is lower case, and has the
# same name as the module (file), such that when we import the function
# it clobbers the file name as the import.
# conda install mrbayes -c bioconda # conda install py3.7 is messy...
# conda install raxml -c bioconda
# conda install fasttree -c bioconda # needs OMP version support...
# conda install scikit-learn -c bioconda
# conda install sratools -c bioconda
# conda install treemix -c bioconda
# conda install toytree -c eaton-lab
# conda install tetrad -c eaton-lab
# conda install structure -c ipyrad
# conda install clumpp -c ipyrad
# conda install bucky -c ipyrad
# conda install bpp -c ipyrad
# tested in 0.9.10
from .raxml import Raxml as raxml
from .mrbayes import MrBayes as mrbayes
from .treemix import Treemix as treemix
from .pca import PCA as pca
from .snps_extracter import SNPsExtracter as snps_extracter
from .snps_imputer import SNPsImputer as snps_imputer
from .treeslider import TreeSlider as treeslider
from .distance import Distance as distance
from .structure import Structure as structure
from .sratools import SRA as sratools
from .vcf_to_hdf5 import VCFtoHDF5 as vcf_to_hdf5 # tetrad version ahead.
# testing
from .locus_extracter import LocusExtracter as locus_extracter
from .tetrad import Tetrad as tetrad
from .window_extracter import WindowExtracter as window_extracter
from .clade_weights import CladeWeights as clade_weights
from .digest_genome import DigestGenome as digest_genome
from .bucky import Bucky as bucky
from .bpp import Bpp as bpp
from .fasttree import Fasttree as fasttree
from .baba import Baba as baba
from .baba2 import Baba as baba2
from .coverage import Coverage as coverage
# from .momi import Momi as momi
# from .eems import Eems as eems
# from .popgen import Popgen as popgen