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xji3
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add in godambe matrix
1 parent fb2f0d1 commit 753f68c

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-173
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‎.DS_Store

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‎Guess.py

Lines changed: 72 additions & 65 deletions
Original file line numberDiff line numberDiff line change
@@ -24,6 +24,9 @@ def main(args):
2424
save_file = './save/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_Guess_' + str(args.guess) + '_nonclock_save.txt'
2525
log_file = './log/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_Guess_' + str(args.guess) + '_nonclock_log.txt'
2626
summary_file = './summary/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_Guess_' + str(args.guess) + '_nonclock_summary.txt'
27+
gradient_file = './summary/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_Guess_' + str(args.guess) + '_nonclock_gradient.txt'
28+
hessian_file = './summary/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_Guess_' + str(args.guess) + '_nonclock_hessian.txt'
29+
godambe_file = './summary/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_Guess_' + str(args.guess) + '_nonclock_godambe.txt'
2730

2831
initial_tract_length_list = np.log([30.0, 200.0])
2932
guess_lnp = -initial_tract_length_list[args.guess-1]
@@ -50,76 +53,80 @@ def main(args):
5053
#test.unpack_x(x)
5154

5255

53-
test.get_mle()
56+
test.get_mle(stringent_level = 'high')
5457
test.get_individual_summary(summary_file)
5558

59+
Godambe_x = np.array([test.psjsmodel.x_IGC[0] - test.psjsmodel.x_IGC[1], test.psjsmodel.x_IGC[1] - np.log(1.0 - np.exp(test.psjsmodel.x_IGC[1]))])
60+
godambe = test.get_Godambe_matrix(Godambe_x)
61+
np.savetxt(open(godambe_file, 'w+'), np.array(godambe))
62+
test.get_gradient_hessian(Godambe_x, gradient_file, hessian_file)
5663

5764

5865
if __name__ == '__main__':
59-
## parser = argparse.ArgumentParser()
60-
## parser.add_argument('--paralog1', required = True, help = 'Name of the 1st paralog')
61-
## parser.add_argument('--paralog2', required = True, help = 'Name of the 2nd paralog')
62-
## parser.add_argument('--G', type = int, dest = 'guess', default = 1, help = 'Guess case')
63-
## parser.add_argument('--heterogeneity', dest = 'rate_variation', action = 'store_true', help = 'rate heterogeneity control')
64-
## parser.add_argument('--homogeneity', dest = 'rate_variation', action = 'store_false', help = 'rate heterogeneity control')
65-
## parser.add_argument('--coding', dest = 'cdna', action = 'store_true', help = 'coding sequence control')
66-
## parser.add_argument('--noncoding', dest = 'cdna', action = 'store_false', help = 'coding sequence control')
67-
## parser.add_argument('--samecodon', dest = 'allow_same_codon', action = 'store_true', help = 'whether allow pair sites from same codon')
68-
## parser.add_argument('--no-samecodon', dest = 'allow_same_codon', action = 'store_false', help = 'whether allow pair sites from same codon')
69-
##
70-
## main(parser.parse_args())
71-
72-
73-
74-
MyStruct = namedtuple('MyStruct', 'paralog1 paralog2 tract_length dim cdna rate_variation allow_same_codon guess')
75-
args = MyStruct(paralog1 = 'EDN', paralog2 = 'ECP', tract_length = 30.0, dim = 1,
76-
cdna = True, rate_variation = True, allow_same_codon = True,
77-
guess = 2)
78-
79-
paralog = [args.paralog1, args.paralog2]
80-
81-
gene_to_orlg_file = './' + '_'.join(paralog) +'_GeneToOrlg.txt'
82-
alignment_file = './' + '_'.join(paralog) +'_Cleaned_input.fasta'
83-
84-
tree_newick = './input_tree.newick'
85-
DupLosList = './EDN_ECP_DupLost.txt'
86-
terminal_node_list = ['Tamarin', 'Macaque', 'Orangutan', 'Gorilla', 'Chimpanzee']
87-
node_to_pos = {'D1':0}
88-
pm_model = 'HKY'
89-
90-
IGC_pm = 'One rate'
91-
seq_index_file = './' + '_'.join(paralog) +'_seq_index.txt'
92-
averaged_x = np.loadtxt('./EDN_ECP_JS_HKY_One_rate_nonclock_save.txt')
93-
averaged_x_js, averaged_x_rates = averaged_x[:5], averaged_x[5:]
94-
95-
save_file = './save/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_Guess_' + str(args.guess) + '_nonclock_save.txt'
96-
log_file = './log/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_Guess_' + str(args.guess) + '_nonclock_log.txt'
97-
summary_file = './summary/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_Guess_' + str(args.guess) + '_nonclock_summary.txt'
98-
99-
initial_tract_length_list = np.log([30.0, 200.0])
100-
guess_lnp = -initial_tract_length_list[args.guess-1]
66+
parser = argparse.ArgumentParser()
67+
parser.add_argument('--paralog1', required = True, help = 'Name of the 1st paralog')
68+
parser.add_argument('--paralog2', required = True, help = 'Name of the 2nd paralog')
69+
parser.add_argument('--G', type = int, dest = 'guess', default = 1, help = 'Guess case')
70+
parser.add_argument('--heterogeneity', dest = 'rate_variation', action = 'store_true', help = 'rate heterogeneity control')
71+
parser.add_argument('--homogeneity', dest = 'rate_variation', action = 'store_false', help = 'rate heterogeneity control')
72+
parser.add_argument('--coding', dest = 'cdna', action = 'store_true', help = 'coding sequence control')
73+
parser.add_argument('--noncoding', dest = 'cdna', action = 'store_false', help = 'coding sequence control')
74+
parser.add_argument('--samecodon', dest = 'allow_same_codon', action = 'store_true', help = 'whether allow pair sites from same codon')
75+
parser.add_argument('--no-samecodon', dest = 'allow_same_codon', action = 'store_false', help = 'whether allow pair sites from same codon')
10176

102-
if args.rate_variation:
103-
x_js = np.concatenate((averaged_x_js[:-1], np.log([0.7, 3.0]), [averaged_x_js[-1] + guess_lnp, guess_lnp]))
104-
if args.allow_same_codon:
105-
save_file = save_file.replace('_nonclock', '_rv_SCOK_nonclock')
106-
log_file = log_file.replace('_nonclock', '_rv_SCOK_nonclock')
107-
summary_file = summary_file.replace('_nonclock', '_rv_SCOK_nonclock')
108-
else:
109-
save_file = save_file.replace('_nonclock', '_rv_NOSC_nonclock')
110-
log_file = log_file.replace('_nonclock', '_rv_SCOK_nonclock')
111-
summary_file = summary_file.replace('_nonclock', '_rv_NOSC_nonclock')
112-
else:
113-
x_js = np.concatenate((averaged_x_js[:-1], [averaged_x_js[-1] + guess_lnp, guess_lnp]))
114-
115-
116-
117-
118-
test = PSJSGeneconv(alignment_file, gene_to_orlg_file, seq_index_file, args.cdna, args.allow_same_codon, tree_newick, DupLosList, x_js, pm_model, IGC_pm,
119-
args.rate_variation, node_to_pos, terminal_node_list, save_file, log_file)
120-
#x = np.concatenate((x_js, averaged_x_rates))
121-
#test.unpack_x(x)
77+
main(parser.parse_args())
12278

79+
12380

124-
test.get_mle()
125-
test.get_individual_summary(summary_file)
81+
## MyStruct = namedtuple('MyStruct', 'paralog1 paralog2 tract_length dim cdna rate_variation allow_same_codon guess')
82+
## args = MyStruct(paralog1 = 'EDN', paralog2 = 'ECP', tract_length = 30.0, dim = 1,
83+
## cdna = True, rate_variation = True, allow_same_codon = True,
84+
## guess = 2)
85+
##
86+
## paralog = [args.paralog1, args.paralog2]
87+
##
88+
## gene_to_orlg_file = './' + '_'.join(paralog) +'_GeneToOrlg.txt'
89+
## alignment_file = './' + '_'.join(paralog) +'_Cleaned_input.fasta'
90+
##
91+
## tree_newick = './input_tree.newick'
92+
## DupLosList = './EDN_ECP_DupLost.txt'
93+
## terminal_node_list = ['Tamarin', 'Macaque', 'Orangutan', 'Gorilla', 'Chimpanzee']
94+
## node_to_pos = {'D1':0}
95+
## pm_model = 'HKY'
96+
##
97+
## IGC_pm = 'One rate'
98+
## seq_index_file = './' + '_'.join(paralog) +'_seq_index.txt'
99+
## averaged_x = np.loadtxt('./EDN_ECP_JS_HKY_One_rate_nonclock_save.txt')
100+
## averaged_x_js, averaged_x_rates = averaged_x[:5], averaged_x[5:]
101+
##
102+
## save_file = './save/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_Guess_' + str(args.guess) + '_nonclock_save.txt'
103+
## log_file = './log/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_Guess_' + str(args.guess) + '_nonclock_log.txt'
104+
## summary_file = './summary/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_Guess_' + str(args.guess) + '_nonclock_summary.txt'
105+
##
106+
## initial_tract_length_list = np.log([30.0, 200.0])
107+
## guess_lnp = -initial_tract_length_list[args.guess-1]
108+
##
109+
## if args.rate_variation:
110+
## x_js = np.concatenate((averaged_x_js[:-1], np.log([0.7, 3.0]), [averaged_x_js[-1] + guess_lnp, guess_lnp]))
111+
## if args.allow_same_codon:
112+
## save_file = save_file.replace('_nonclock', '_rv_SCOK_nonclock')
113+
## log_file = log_file.replace('_nonclock', '_rv_SCOK_nonclock')
114+
## summary_file = summary_file.replace('_nonclock', '_rv_SCOK_nonclock')
115+
## else:
116+
## save_file = save_file.replace('_nonclock', '_rv_NOSC_nonclock')
117+
## log_file = log_file.replace('_nonclock', '_rv_SCOK_nonclock')
118+
## summary_file = summary_file.replace('_nonclock', '_rv_NOSC_nonclock')
119+
## else:
120+
## x_js = np.concatenate((averaged_x_js[:-1], [averaged_x_js[-1] + guess_lnp, guess_lnp]))
121+
##
122+
##
123+
##
124+
##
125+
## test = PSJSGeneconv(alignment_file, gene_to_orlg_file, seq_index_file, args.cdna, args.allow_same_codon, tree_newick, DupLosList, x_js, pm_model, IGC_pm,
126+
## args.rate_variation, node_to_pos, terminal_node_list, save_file, log_file)
127+
## #x = np.concatenate((x_js, averaged_x_rates))
128+
## #test.unpack_x(x)
129+
##
130+
##
131+
## test.get_mle()
132+
## test.get_individual_summary(summary_file)

‎Run_Force.py

Lines changed: 96 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,96 @@
1+
from IGCexpansion.PSJSGeneconv import *
2+
from IGCexpansion.JSGeneconv import *
3+
import argparse
4+
from collections import namedtuple
5+
import numpy as np
6+
7+
def main(args):
8+
paralog = [args.paralog1, args.paralog2]
9+
10+
gene_to_orlg_file = './' + '_'.join(paralog) +'_GeneToOrlg.txt'
11+
alignment_file = './' + '_'.join(paralog) +'_Cleaned_input.fasta'
12+
13+
tree_newick = './input_tree.newick'
14+
DupLosList = './EDN_ECP_DupLost.txt'
15+
terminal_node_list = ['Tamarin', 'Macaque', 'Orangutan', 'Gorilla', 'Chimpanzee']
16+
node_to_pos = {'D1':0}
17+
pm_model = 'HKY'
18+
19+
IGC_pm = 'One rate'
20+
seq_index_file = './' + '_'.join(paralog) +'_seq_index.txt'
21+
22+
if args.rate_variation:
23+
save_file = './save/JS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_rv_nonclock_save.txt'
24+
log_file = './log/JS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_rv_nonclock_log.txt'
25+
summary_file = './summary/JS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_rv_nonclock_summary.txt'
26+
x_js = np.log([ 0.5, 0.5, 0.5, 4.35588244, 0.5, 5.0, 0.3])
27+
else:
28+
save_file = './save/JS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_nonclock_save.txt'
29+
log_file = './log/JS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_nonclock_log.txt'
30+
summary_file = './summary/JS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_nonclock_summary.txt'
31+
x_js = np.log([ 0.5, 0.5, 0.5, 4.35588244, 0.3])
32+
33+
34+
35+
test_JS = JSGeneconv(alignment_file, gene_to_orlg_file, args.cdna, tree_newick, DupLosList, x_js, pm_model, IGC_pm,
36+
args.rate_variation, node_to_pos, terminal_node_list, save_file, log_file = log_file)
37+
test_JS.get_mle()
38+
#test_JS.get_expectedNumGeneconv()
39+
test_JS.get_individual_summary(summary_file)
40+
41+
42+
43+
if __name__ == '__main__':
44+
## parser = argparse.ArgumentParser()
45+
## parser.add_argument('--paralog1', required = True, help = 'Name of the 1st paralog')
46+
## parser.add_argument('--paralog2', required = True, help = 'Name of the 2nd paralog')
47+
## parser.add_argument('--L', type = float, dest = 'tract_length', default = 30.0, help = 'Initial guess tract length')
48+
## parser.add_argument('--D', type = int, dest = 'dim', default = 0, help = 'Dimension used in search with default value 0')
49+
## parser.add_argument('--heterogeneity', dest = 'rate_variation', action = 'store_true', help = 'rate heterogeneity control')
50+
## parser.add_argument('--homogeneity', dest = 'rate_variation', action = 'store_false', help = 'rate heterogeneity control')
51+
## parser.add_argument('--coding', dest = 'cdna', action = 'store_true', help = 'coding sequence control')
52+
## parser.add_argument('--noncoding', dest = 'cdna', action = 'store_false', help = 'coding sequence control')
53+
## parser.add_argument('--samecodon', dest = 'allow_same_codon', action = 'store_true', help = 'whether allow pair sites from same codon')
54+
## parser.add_argument('--no-samecodon', dest = 'allow_same_codon', action = 'store_false', help = 'whether allow pair sites from same codon')
55+
##
56+
## main(parser.parse_args())
57+
58+
59+
60+
MyStruct = namedtuple('MyStruct', 'paralog1 paralog2 tract_length dim cdna rate_variation allow_same_codon')
61+
args = MyStruct(paralog1 = 'EDN', paralog2 = 'ECP', tract_length = 30.0, dim = 1, cdna = True, rate_variation = True, allow_same_codon = True)
62+
63+
paralog = [args.paralog1, args.paralog2]
64+
65+
gene_to_orlg_file = './' + '_'.join(paralog) +'_GeneToOrlg.txt'
66+
alignment_file = './' + '_'.join(paralog) +'_Cleaned_input.fasta'
67+
68+
tree_newick = './input_tree.newick'
69+
DupLosList = './EDN_ECP_DupLost.txt'
70+
terminal_node_list = ['Tamarin', 'Macaque', 'Orangutan', 'Gorilla', 'Chimpanzee']
71+
node_to_pos = {'D1':0}
72+
pm_model = 'HKY'
73+
74+
IGC_pm = 'One rate'
75+
seq_index_file = './' + '_'.join(paralog) +'_seq_index.txt'
76+
77+
force = {6:0.0}
78+
if args.rate_variation:
79+
save_file = './save/Force_JS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_rv_nonclock_save.txt'
80+
log_file = './log/Force_JS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_rv_nonclock_log.txt'
81+
summary_file = './summary/Force_JS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_rv_nonclock_summary.txt'
82+
x_js = np.log([ 0.5, 0.5, 0.5, 4.35588244, 0.5, 5.0, 0.3])
83+
else:
84+
save_file = './save/Force_JS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_nonclock_save.txt'
85+
log_file = './log/Force_JS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_nonclock_log.txt'
86+
summary_file = './summary/Force_JS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_nonclock_summary.txt'
87+
x_js = np.log([ 0.5, 0.5, 0.5, 4.35588244, 0.3])
88+
89+
90+
91+
test_JS = JSGeneconv(alignment_file, gene_to_orlg_file, args.cdna, tree_newick, DupLosList, x_js, pm_model, IGC_pm,
92+
args.rate_variation, node_to_pos, terminal_node_list, save_file, force = force)
93+
test_JS.get_mle()
94+
#test_JS.get_expectedNumGeneconv()
95+
test_JS.get_individual_summary(summary_file)
96+

‎Run_IS_IGC.py

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -52,3 +52,4 @@ def main(args):
5252
test_force.update_by_x(test.x)
5353
test_force._loglikelihood2()
5454
test_force.get_sitewise_loglikelihood_summary('./Summary/Force_' + '_'.join(paralog) + '_Ind_MG94_nonclock_sw_lnL.txt')
55+

‎Run_PSJS.py

Lines changed: 17 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -49,16 +49,25 @@ def main(args):
4949
save_file = './save/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_init_' + str(args.tract_length) + '_nonclock_save.txt'
5050
log_file = './log/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_init_' + str(args.tract_length) + '_nonclock_log.txt'
5151
summary_file = './summary/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_init_' + str(args.tract_length) + '_nonclock_summary.txt'
52+
gradient_file = './summary/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_init_' + str(args.tract_length) + '_nonclock_gradient.txt'
53+
hessian_file = './summary/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_init_' + str(args.tract_length) + '_nonclock_hessian.txt'
54+
godambe_file = './summary/PSJS_HKY_'+ '_'.join(paralog) + '_' + IGC_pm.replace(' ', '_') + '_init_' + str(args.tract_length) + '_nonclock_godambe.txt'
5255

5356
if args.rate_variation:
5457
if args.allow_same_codon:
5558
save_file = save_file.replace('_nonclock', '_rv_SCOK_nonclock')
5659
log_file = log_file.replace('_nonclock', '_rv_SCOK_nonclock')
5760
summary_file = summary_file.replace('_nonclock', '_rv_SCOK_nonclock')
61+
gradient_file = gradient_file.replace('_nonclock', '_rv_SCOK_nonclock')
62+
hessian_file = hessian_file.replace('_nonclock', '_rv_SCOK_nonclock')
63+
godambe_file = godambe_file.replace('_nonclock', '_rv_SCOK_nonclock')
5864
else:
5965
save_file = save_file.replace('_nonclock', '_rv_NOSC_nonclock')
6066
log_file = log_file.replace('_nonclock', '_rv_NOSC_nonclock')
6167
summary_file = summary_file.replace('_nonclock', '_rv_NOSC_nonclock')
68+
gradient_file = summary_file.replace('_nonclock', '_rv_NOSC_nonclock')
69+
hessian_file = hessian_file.replace('_nonclock', '_rv_NOSC_nonclock')
70+
godambe_file = godambe_file.replace('_nonclock', '_rv_NOSC_nonclock')
6271

6372

6473
force = None
@@ -67,10 +76,10 @@ def main(args):
6776
[ test_JS.jsmodel.x_js[-1] - np.log(args.tract_length), - np.log(args.tract_length) ]))
6877
test = PSJSGeneconv(alignment_file, gene_to_orlg_file, seq_index_file, args.cdna, args.allow_same_codon, tree_newick, DupLosList, x_js, pm_model, IGC_pm,
6978
args.rate_variation, node_to_pos, terminal_node_list, save_file, log_file, force)
70-
x = np.concatenate((test_JS.jsmodel.x_js[:-1], \
71-
[ test_JS.jsmodel.x_js[-1] - np.log(args.tract_length), - np.log(args.tract_length) ],
72-
test_JS.x[len(test_JS.jsmodel.x_js):]))
73-
test.unpack_x(x)
79+
## x = np.concatenate((test_JS.jsmodel.x_js[:-1], \
80+
## [ test_JS.jsmodel.x_js[-1] - np.log(args.tract_length), - np.log(args.tract_length) ],
81+
## test_JS.x[len(test_JS.jsmodel.x_js):]))
82+
## test.unpack_x(x)
7483

7584
if args.dim == 1:
7685
test.optimize_x_IGC(dimension = 1)
@@ -83,7 +92,10 @@ def main(args):
8392
pairwise_lnL_summary_file = summary_file.replace('_summary.txt', '_lnL_summary.txt')
8493
test.get_pairwise_loglikelihood_summary(pairwise_lnL_summary_file)
8594

86-
95+
Godambe_x = np.array([test.psjsmodel.x_IGC[0] - test.psjsmodel.x_IGC[1], test.psjsmodel.x_IGC[1] - np.log(1.0 - np.exp(test.psjsmodel.x_IGC[1]))])
96+
godambe = test.get_Godambe_matrix(Godambe_x)
97+
np.savetxt(open(godambe_file, 'w+'), np.array(godambe))
98+
test.get_gradient_hessian(Godambe_x, gradient_file, hessian_file)
8799

88100

89101
if __name__ == '__main__':

‎Summary/Force_JS_HKY_EDN_ECP_One_rate_rv_nonclock_summary.txt

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@@ -0,0 +1,20 @@
1+
-1.725666825303625046e+03
2+
4.710000000000000000e+02
3+
2.832183938316048533e-01
4+
2.539763087867064062e-01
5+
2.096056199406600984e-01
6+
2.531996774410285589e-01
7+
2.130777585861938661e+00
8+
1.602457590771226181e+00
9+
1.494351768760043164e+00
10+
0.000000000000000000e+00
11+
3.550151737220051673e-02
12+
8.651243137184438589e-03
13+
7.786118823465996985e-02
14+
4.364041283424922174e-02
15+
1.103757449799982159e-02
16+
1.106390738863533181e-02
17+
2.454132190459420299e-02
18+
4.159627308636074973e-03
19+
4.602389296307361592e-03
20+
# ll length Pi_A Pi_C Pi_G Pi_T kappa r2 r3 Tau D1__N1 N0__D1 N0__Tamarin N1__Macaque N1__N2 N2__N3 N2__Orangutan N3__Chimpanzee N3__Gorilla

‎Summary/JS_HKY_EDN_ECP_One_rate_rv_nonclock_summary.txt

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@@ -1,20 +1,20 @@
1-
-1.713060332022836519e+03
1+
-1.713060331840455774e+03
22
4.710000000000000000e+02
3-
2.803270798801004160e-01
4-
2.550627345068984808e-01
5-
2.088813478289951175e-01
6-
2.557288377840059579e-01
7-
2.114846419051784832e+00
8-
1.518907731452042276e+00
9-
1.557830448702122617e+00
10-
2.431542390738316239e+00
11-
5.254910608330801147e-02
12-
7.668122112290930333e-03
13-
6.901309901061838947e-02
14-
3.819609457290611826e-02
15-
6.277989212778250193e-03
16-
8.145961790921842083e-03
17-
2.213974992859549240e-02
18-
3.381341174629142257e-03
19-
3.713409118298241409e-03
3+
2.803334564183099231e-01
4+
2.550568720163197134e-01
5+
2.088866733214117533e-01
6+
2.557229982439586102e-01
7+
2.114845098926028566e+00
8+
1.518907807302463331e+00
9+
1.557833249293013589e+00
10+
2.431535833792237700e+00
11+
5.254893087480514563e-02
12+
7.668148614098987438e-03
13+
6.901333752689087220e-02
14+
3.819613210906895595e-02
15+
6.277926983064822768e-03
16+
8.146003311252529577e-03
17+
2.213969672860374716e-02
18+
3.381356822886472362e-03
19+
3.713435306738357977e-03
2020
# ll length Pi_A Pi_C Pi_G Pi_T kappa r2 r3 Tau D1__N1 N0__D1 N0__Tamarin N1__Macaque N1__N2 N2__N3 N2__Orangutan N3__Chimpanzee N3__Gorilla

‎Summary/PSJS_HKY_EDN_ECP_One_rate_Guess_1_nonclock_godambe.txt

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@@ -0,0 +1,2 @@
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8.032818425839866050e-02 9.319319424641088766e-06
2+
9.319319424641090460e-06 7.096238894146725186e-05

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