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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
    consense_out = phy_file.rsplit(".",1)[0] + ".consensustree.nodesupport"
    e = phy_file.rsplit(".",1)[0] + ".fconsense"
    consense_cl = FConsenseCommandline(FPHYLIP_BIN("fconsense"), \
        intreefile=neighbor_out, outfile=e, outtreefile=consense_out)
    stdout, stderr = consense_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
 
    def test_fconsense(self):
        """Calculate a consensus tree with fconsense"""
        cline = FConsenseCommandline(exes["fconsense"],
                                     intreefile = "Phylip/horses.tree",
                                     outtreefile = "test_file",
                                     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
 
    def test_fconsense(self):
        """Calculate a consensus tree with fconsense"""
        cline = FConsenseCommandline(exes["fconsense"],
                                     intreefile = "Phylip/horses.tree",
                                     outtreefile = "test_file",
                                     auto = True, filter = True)
        stdout, stderr = cline()