def ancestral_sequence_inference(tree=None,
aln=None,
ref=None,
infer_gtr=True,
marginal=False,
optimize_branch_length=True,
branch_length_mode='auto'):
from treetime import TreeAnc
tt = TreeAnc(tree=tree, aln=aln, ref=ref, gtr='JC69', verbose=1)
#convert marginal (from args.ancestral) from 'joint' or 'marginal' to True or False
bool_marginal = (marginal == "marginal")
if optimize_branch_length:
tt.optimize_seq_and_branch_len(infer_gtr=infer_gtr,
marginal_sequences=bool_marginal,
branch_length_mode=branch_length_mode)
else: # only infer ancestral sequences, leave branch length untouched
tt.infer_ancestral_sequences(infer_gtr=infer_gtr,
marginal=bool_marginal)
print(
"\nInferred ancestral sequence states using TreeTime:"
"\n\tSagulenko et al. TreeTime: Maximum-likelihood phylodynamic analysis"
"\n\tVirus Evolution, vol 4, https://academic.oup.com/ve/article/4/1/vex042/4794731\n"
)
return tt
def ancestral_sequence_inference(tree=None, aln=None, infer_gtr=True,
optimize_branch_length=True):
from treetime import TreeAnc
tt = TreeAnc(tree=tree, aln=aln, gtr='JC69')
if optimize_branch_length:
tt.optimize_seq_and_branch_len(infer_gtr=infer_gtr)
else: # only infer ancestral sequences, leave branch length untouched
tt.infer_ancestral_sequences(infer_gtr=infer_gtr)
return tt
