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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
 
    dnadist_out = phy_file.rsplit(".",1)[0] + ".fdnadist"
    dnadist_cl = FDNADistCommandline(FPHYLIP_BIN("fdnadist"), \
        sequence=seqboot_out, outfile=dnadist_out, method="f")
    stdout, stderr = dnadist_cl()
    # distance without bootstrapping
    dnadist_out0 = phy_file.rsplit(".",1)[0] + ".fdnadist0"
    dnadist_cl0 = FDNADistCommandline(FPHYLIP_BIN("fdnadist"), \
        sequence=phy_file, outfile=dnadist_out0, method="f")
    stdout, stderr = dnadist_cl0()

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 distances_from_alignment(self, filename, DNA = True):
        """check we can make distance matrix from a given alignment"""
        self.assertTrue(os.path.isfile(filename), "Missing %s" % filename)
        if DNA:
            cline = FDNADistCommandline(exes["fdnadist"],

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 distances_from_alignment(self, filename, DNA = True):
        """check we can make distance matrix from a given alignment"""
        self.assertTrue(os.path.isfile(filename), "Missing %s" % filename)
        if DNA:
            cline = FDNADistCommandline(exes["fdnadist"],