def __init__(self, raxml_args="-T 2 --JC69 -c 1"):
self.raxml_args = [raxml_args]
if platform.system() == 'Windows':
# Windows version:
raxml_path = os.path.join(SPECTRALTREE_RAXML_PATH,
'raxmlHPC-SSE3.exe')
elif platform.system() == 'Darwin':
#MacOS version:
raxml_path = os.path.join(SPECTRALTREE_RAXML_PATH,
'raxmlHPC-macOS')
elif platform.system() == 'Linux':
#Linux version
raxml_path = os.path.join(SPECTRALTREE_RAXML_PATH,
'raxmlHPC-SSE3-linux')
else:
raise OSError(
f"Cannot identify operating system {platform.system()}.")
self._rx = raxml.RaxmlRunner(raxml_path=raxml_path)
import dendropy
from dendropy.interop import raxml
pleth = dendropy.DnaCharacterMatrix.get(
path="../data/full_plethodon_alignment.phy",
schema="fasta"
)
rx = raxml.RaxmlRunner(raxml_path="/bin/raxmlHPC")
tree = rx.estimate_tree(
char_matrix=pleth)
tree.write_to_path("../data_output/tree.phy", schema="newick")
#! /usr/bin/env python
import dendropy
from dendropy.interop import raxml
data = dendropy.DnaCharacterMatrix.get_from_path("pythonidae.nex", "nexus")
rx = raxml.RaxmlRunner()
tree = rx.estimate_tree(data)
## TEST WITHOUT CLASS
###########################################################################
from dendropy.interop import raxml
reference_tree = utils.balanced_binary(16)
data = simulate_discrete_chars(
1000,
reference_tree,
Jc69(),
mutation_rate=generation.Jukes_Cantor().p2t(0.95),
)
if platform.system() == 'Windows':
# Windows version:
rx = raxml.RaxmlRunner(raxml_path=os.path.join(
os.path.dirname(sys.path[0]), r'spectraltree\raxmlHPC-SSE3.exe'))
elif platform.system() == 'Darwin':
#MacOS version:
rx = raxml.RaxmlRunner(raxml_path=os.path.join(
os.path.dirname(sys.path[0]), 'spectraltree/raxmlHPC-macOS'))
elif platform.system() == 'Linux':
#Linux version
rx = raxml.RaxmlRunner(raxml_path=os.path.join(
os.path.dirname(sys.path[0]), 'spectraltree/raxmlHPC-SSE3-linux'))
tree = rx.estimate_tree(char_matrix=data, raxml_args=["-T 2"])
type(data)
#tree.print_plot()