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src/c/o/cogent-1.5.3/tests/test_evolve/test_likelihood_function.py   cogent(Download)
    def setUp(self):
        self.alignment = ALIGNMENT.takeSeqs(OTU_NAMES)[0: 42]
        self.tree = LoadTree(tip_names=OTU_NAMES)
 
    def _makeLikelihoodFunction(self, submod, translate=False, **kw):

src/p/y/pycogent-HEAD/tests/test_evolve/test_likelihood_function.py   pycogent(Download)
    def setUp(self):
        self.alignment = ALIGNMENT.takeSeqs(OTU_NAMES)[0: 42]
        self.tree = LoadTree(tip_names=OTU_NAMES)
 
    def _makeLikelihoodFunction(self, submod, translate=False, **kw):

src/p/y/pycogent-HEAD/tests/test_evolve/test_bootstrap.py   pycogent(Download)
                filename = os.path.join(data_path, "brca1.fasta"),
                moltype = moltype)
        return alignmentobj.takeSeqs(seqnames)[:1000]
 
    def getcontroller(self,treeobj, submodobj):

src/c/o/cogent-1.5.3/tests/test_evolve/test_bootstrap.py   cogent(Download)
                filename = os.path.join(data_path, "brca1.fasta"),
                moltype = moltype)
        return alignmentobj.takeSeqs(seqnames)[:1000]
 
    def getcontroller(self,treeobj, submodobj):