Bio.Phylo.Applications.PhymlCommandline

All Samples(9) | Call(6) | Derive(0) | Import(3)

src/j/c/jcvi-HEAD/apps/phylo.py jcvi(Download)

from Bio.Emboss.Applications import FSeqBootCommandline, FDNADistCommandline, \
            FNeighborCommandline, FConsenseCommandline
from Bio.Phylo.Applications import PhymlCommandline, RaxmlCommandline
 
from jcvi.apps.ks import AbstractCommandline, find_first_isoform, \

    AlignIO.write(alignment, file(phy_file, "w"), "phylip-relaxed")
 
    phyml_cl = PhymlCommandline(cmd=PHYML_BIN("phyml"), input=phy_file, **kwargs)
    logging.debug("Building ML tree using PhyML: %s" % phyml_cl)
    stdout, stderr = phyml_cl()

src/b/i/biopython-1.63/Tests/test_phyml_tool.py biopython(Download)

 
from Bio import Phylo
from Bio.Phylo.Applications import PhymlCommandline
from Bio import MissingExternalDependencyError

    def test_phyml(self):
        """Run PhyML using the wrapper."""
        cmd = PhymlCommandline(phyml_exe, input=EX_PHYLIP, datatype='aa')
        # Smoke test
        try:
            out, err = cmd()

src/b/i/biopython-HEAD/Tests/test_phyml_tool.py biopython(Download)

 
from Bio import Phylo
from Bio.Phylo.Applications import PhymlCommandline
from Bio import MissingExternalDependencyError

    def test_phyml(self):
        """Run PhyML using the wrapper."""
        cmd = PhymlCommandline(phyml_exe, input=EX_PHYLIP, datatype='aa')
        # Smoke test
        try:
            out, err = cmd()