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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
 
    seqboot_out = phy_file.rsplit(".",1)[0] + ".fseqboot"
    seqboot_cl = FSeqBootCommandline(FPHYLIP_BIN("fseqboot"), \
        sequence=phy_file, outfile=seqboot_out, \
        seqtype="d", reps=100, seed=12345)
    stdout, stderr = seqboot_cl()

src/b/i/biopython-1.63/Tests/test_EmbossPhylipNew.py   biopython(Download)
 
from Bio.Emboss.Applications import FDNADistCommandline, FNeighborCommandline
from Bio.Emboss.Applications import FSeqBootCommandline, FProtDistCommandline
from Bio.Emboss.Applications import FProtParsCommandline, FConsenseCommandline
from Bio.Emboss.Applications import FTreeDistCommandline, FDNAParsCommandline
        """
        self.assertTrue(os.path.isfile(filename), "Missing %s" % filename)
        cline = FSeqBootCommandline(exes["fseqboot"],
                                    sequence = filename,
                                    outfile = "test_file",
                                    seqtype = align_type,
                                    reps = 2,
                                    auto = True, filter = True)
        stdout, stderr = cline()

src/b/i/biopython-HEAD/Tests/test_EmbossPhylipNew.py   biopython(Download)
 
from Bio.Emboss.Applications import FDNADistCommandline, FNeighborCommandline
from Bio.Emboss.Applications import FSeqBootCommandline, FProtDistCommandline
from Bio.Emboss.Applications import FProtParsCommandline, FConsenseCommandline
from Bio.Emboss.Applications import FTreeDistCommandline, FDNAParsCommandline
        """
        self.assertTrue(os.path.isfile(filename), "Missing %s" % filename)
        cline = FSeqBootCommandline(exes["fseqboot"],
                                    sequence = filename,
                                    outfile = "test_file",
                                    seqtype = align_type,
                                    reps = 2,
                                    auto = True, filter = True)
        stdout, stderr = cline()