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src/j/c/jcvi-HEAD/apps/phylo.py   jcvi(Download)
from Bio import SeqIO, AlignIO
from Bio.Data import CodonTable
from Bio.Emboss.Applications import FSeqBootCommandline, FDNADistCommandline, \
            FNeighborCommandline, FConsenseCommandline
from Bio.Phylo.Applications import PhymlCommandline, RaxmlCommandline
    neighbor_out = phy_file.rsplit(".",1)[0] + ".njtree"
    e = phy_file.rsplit(".",1)[0] + ".fneighbor"
    neighbor_cl = FNeighborCommandline(FPHYLIP_BIN("fneighbor"), \
        datafile=dnadist_out, outfile=e, outtreefile=neighbor_out)
    stdout, stderr = neighbor_cl()

src/b/i/biopython-1.63/Tests/test_EmbossPhylipNew.py   biopython(Download)
from Bio.Nexus import Trees # One day we should use planned TreeIO module
 
from Bio.Emboss.Applications import FDNADistCommandline, FNeighborCommandline
from Bio.Emboss.Applications import FSeqBootCommandline, FProtDistCommandline
from Bio.Emboss.Applications import FProtParsCommandline, FConsenseCommandline
    def tree_from_distances(self, filename):
        """Check we can estimate a tree from a distance matrix"""
        self.assertTrue(os.path.isfile(filename), "Missing %s" % filename)
        cline = FNeighborCommandline(exes["fneighbor"],
                                     datafile = filename,
                                     outtreefile = "test_file",
                                     auto= True, filter = True)
        stdout, stderr = cline()

src/b/i/biopython-HEAD/Tests/test_EmbossPhylipNew.py   biopython(Download)
from Bio.Nexus import Trees # One day we should use planned TreeIO module
 
from Bio.Emboss.Applications import FDNADistCommandline, FNeighborCommandline
from Bio.Emboss.Applications import FSeqBootCommandline, FProtDistCommandline
from Bio.Emboss.Applications import FProtParsCommandline, FConsenseCommandline
    def tree_from_distances(self, filename):
        """Check we can estimate a tree from a distance matrix"""
        self.assertTrue(os.path.isfile(filename), "Missing %s" % filename)
        cline = FNeighborCommandline(exes["fneighbor"],
                                     datafile = filename,
                                     outtreefile = "test_file",
                                     auto= True, filter = True)
        stdout, stderr = cline()