TreeTime
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TreeTime command line usage
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API documentation
TreeTime
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Index
_
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A
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B
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C
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E
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G
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I
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L
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M
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O
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P
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R
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S
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T
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W
_
__init__() (treetime.ClockTree method)
(treetime.Coalescent method)
(treetime.GTR method)
(treetime.seqgen.SeqGen method)
(treetime.TreeAnc method)
(treetime.TreeTime method)
A
aln() (treetime.TreeAnc method)
assign_rates() (treetime.GTR method)
B
branch_length_to_years() (treetime.ClockTree method)
branch_merger_rate() (treetime.Coalescent method)
C
clock_filter() (treetime.TreeTime method)
ClockTree (class in treetime)
Coalescent (class in treetime)
convert_dates() (treetime.ClockTree method)
cost() (treetime.Coalescent method)
custom() (treetime.GTR class method)
E
expQt() (treetime.GTR method)
G
get_confidence_interval() (treetime.ClockTree method)
get_max_posterior_region() (treetime.ClockTree method)
get_tree_dict() (treetime.TreeAnc method)
GTR (class in treetime)
gtr() (treetime.TreeAnc method)
I
infer() (treetime.GTR class method)
infer_ancestral_sequences() (treetime.TreeAnc method)
infer_gtr() (treetime.TreeAnc method)
init_date_constraints() (treetime.ClockTree method)
L
leaves_lookup() (treetime.TreeAnc method)
logger() (treetime.TreeAnc method)
M
make_time_tree() (treetime.ClockTree method)
module
treetime
O
optimal_t() (treetime.GTR method)
optimal_t_compressed() (treetime.GTR method)
optimize_skyline() (treetime.Coalescent method)
optimize_tree() (treetime.TreeAnc method)
P
plot_root_to_tip() (treetime.TreeTime method)
plot_vs_years() (in module treetime)
prepare_tree() (treetime.TreeAnc method)
print_lh() (treetime.TreeTime method)
prob_t() (treetime.GTR method)
prob_t_compressed() (treetime.GTR method)
prob_t_profiles() (treetime.GTR method)
prof2seq() (in module treetime.seq_utils)
propagate_profile() (treetime.GTR method)
prune_short_branches() (treetime.TreeAnc method)
R
random() (treetime.GTR class method)
read_vcf() (in module treetime.vcf_utils)
relaxed_clock() (treetime.TreeTime method)
reroot() (treetime.TreeTime method)
resolve_polytomies() (treetime.TreeTime method)
run() (treetime.TreeTime method)
S
seq2array() (in module treetime.seq_utils)
seq2prof() (in module treetime.seq_utils)
SeqGen (class in treetime.seqgen)
sequence_LH() (treetime.TreeAnc method)
sequence_logLH() (treetime.GTR method)
set_gtr() (treetime.TreeAnc method)
skyline_empirical() (treetime.Coalescent method)
skyline_inferred() (treetime.Coalescent method)
standard() (treetime.GTR static method)
state_pair() (treetime.GTR method)
T
timetree_likelihood() (treetime.ClockTree method)
total_merger_rate() (treetime.Coalescent method)
tree() (treetime.TreeAnc method)
TreeAnc (class in treetime)
treetime
module
TreeTime (class in treetime)
W
write_vcf() (in module treetime.vcf_utils)
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