1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
|
seed used = 1055736305
CODONML (in paml version 4.3, August 2009) ../../Alignments/lysinYangSwanson2002.nuc
Model: One dN/dS ratio for branches (2 genes: separate data)
Codon frequency model: F3x4
ns = 25 ls = 134
Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT 3 3 3 3 3 3 | Ser TCT 1 1 1 1 0 0 | Tyr TAT 2 2 1 2 3 3 | Cys TGT 0 0 0 0 0 0
TTC 3 3 3 3 3 4 | TCC 0 0 0 0 0 0 | TAC 8 8 8 7 6 5 | TGC 0 0 0 0 0 0
Leu TTA 2 2 1 2 1 1 | TCA 0 0 1 1 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
TTG 1 1 1 1 1 1 | TCG 0 1 1 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 4 4 4 5 4 4
--------------------------------------------------------------------------------------------------------------
Leu CTT 1 1 1 1 2 2 | Pro CCT 0 0 0 0 0 0 | His CAT 2 2 1 0 3 2 | Arg CGT 2 2 2 2 2 2
CTC 1 1 1 1 1 1 | CCC 1 1 1 1 1 0 | CAC 1 2 2 2 1 1 | CGC 2 3 3 2 2 2
CTA 0 0 0 0 0 0 | CCA 4 5 3 5 5 5 | Gln CAA 0 0 0 1 1 0 | CGA 0 0 0 1 0 1
CTG 6 6 6 5 5 5 | CCG 1 0 0 0 0 0 | CAG 3 3 3 3 4 4 | CGG 1 1 1 1 1 1
--------------------------------------------------------------------------------------------------------------
Ile ATT 4 4 5 4 3 3 | Thr ACT 1 2 1 2 2 2 | Asn AAT 4 3 5 5 4 5 | Ser AGT 0 0 0 0 0 0
ATC 3 3 4 3 4 4 | ACC 2 2 1 2 1 1 | AAC 2 4 3 2 3 5 | AGC 1 0 0 1 0 1
ATA 1 1 0 1 1 0 | ACA 2 2 2 0 0 0 | Lys AAA 4 4 3 4 4 4 | Arg AGA 7 6 8 7 9 9
Met ATG 7 7 6 8 7 6 | ACG 0 1 1 0 1 1 | AAG 8 7 6 8 6 5 | AGG 0 1 2 1 1 2
--------------------------------------------------------------------------------------------------------------
Val GTT 7 6 5 9 7 5 | Ala GCT 3 2 4 1 2 4 | Asp GAT 5 5 4 4 4 6 | Gly GGT 2 2 1 2 3 2
GTC 3 2 2 1 3 1 | GCC 1 1 1 2 1 2 | GAC 2 1 2 1 3 1 | GGC 2 2 2 2 2 2
GTA 1 1 3 0 1 2 | GCA 3 3 4 3 2 3 | Glu GAA 5 4 4 3 5 3 | GGA 2 3 3 2 2 2
GTG 0 0 0 0 0 2 | GCG 2 2 2 3 2 2 | GAG 0 0 1 2 1 1 | GGG 1 1 0 1 0 0
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------
Phe TTT 3 3 3 3 4 4 | Ser TCT 0 0 0 1 0 0 | Tyr TAT 3 3 4 4 0 1 | Cys TGT 0 0 0 0 0 0
TTC 4 4 3 4 1 1 | TCC 0 0 0 1 2 0 | TAC 5 6 6 5 7 7 | TGC 0 0 0 0 0 0
Leu TTA 1 1 0 1 1 0 | TCA 0 0 0 0 1 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
TTG 1 1 3 2 4 4 | TCG 0 0 0 0 0 1 | TAG 0 0 0 0 0 0 | Trp TGG 4 3 3 4 5 4
--------------------------------------------------------------------------------------------------------------
Leu CTT 2 1 2 1 3 3 | Pro CCT 0 1 1 0 3 2 | His CAT 2 2 2 2 3 2 | Arg CGT 2 4 3 3 5 4
CTC 1 1 1 2 0 0 | CCC 0 0 0 1 1 2 | CAC 1 1 1 1 3 2 | CGC 2 4 4 2 2 2
CTA 0 0 0 0 0 0 | CCA 5 5 4 3 1 2 | Gln CAA 0 0 2 0 3 3 | CGA 1 0 1 2 0 2
CTG 5 6 5 4 2 2 | CCG 0 1 1 1 0 0 | CAG 4 3 4 5 6 4 | CGG 1 1 0 1 0 0
--------------------------------------------------------------------------------------------------------------
Ile ATT 3 5 4 1 3 3 | Thr ACT 2 0 0 3 1 1 | Asn AAT 5 3 9 5 1 2 | Ser AGT 0 2 0 0 0 0
ATC 4 2 2 3 4 4 | ACC 1 2 2 2 1 2 | AAC 5 4 3 3 3 2 | AGC 1 0 0 1 3 4
ATA 0 2 1 3 2 1 | ACA 0 1 0 1 0 0 | Lys AAA 4 2 3 3 3 3 | Arg AGA 8 6 7 7 3 4
Met ATG 6 6 6 6 4 4 | ACG 1 1 1 1 1 1 | AAG 5 6 5 7 4 5 | AGG 2 2 2 1 5 5
--------------------------------------------------------------------------------------------------------------
Val GTT 5 6 5 7 7 7 | Ala GCT 4 1 3 2 2 2 | Asp GAT 6 4 2 3 2 2 | Gly GGT 2 1 2 2 2 2
GTC 1 3 4 2 3 4 | GCC 2 2 1 2 4 4 | GAC 1 1 2 1 1 2 | GGC 2 2 2 2 2 1
GTA 2 1 1 1 1 2 | GCA 2 5 3 6 3 2 | Glu GAA 4 3 4 2 4 4 | GGA 3 3 3 2 1 1
GTG 2 1 2 0 2 3 | GCG 2 1 1 0 0 0 | GAG 1 3 1 0 1 1 | GGG 0 1 0 1 1 1
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------
Phe TTT 4 4 4 4 6 5 | Ser TCT 0 0 0 0 1 0 | Tyr TAT 0 3 0 0 2 2 | Cys TGT 0 0 0 0 0 0
TTC 2 2 2 2 1 1 | TCC 0 3 1 1 0 1 | TAC 5 4 6 6 4 6 | TGC 0 0 0 0 0 0
Leu TTA 0 0 0 0 1 0 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
TTG 4 3 4 4 5 4 | TCG 1 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 4 4 4 4 4 4
--------------------------------------------------------------------------------------------------------------
Leu CTT 3 4 3 3 4 5 | Pro CCT 3 2 2 2 1 2 | His CAT 3 1 2 2 1 2 | Arg CGT 4 5 4 4 7 6
CTC 0 0 0 0 1 1 | CCC 3 1 1 1 1 1 | CAC 3 4 3 3 2 2 | CGC 2 3 3 3 1 1
CTA 1 0 0 0 0 0 | CCA 1 2 2 2 4 3 | Gln CAA 4 1 1 1 2 1 | CGA 2 1 1 1 1 1
CTG 2 3 4 4 2 1 | CCG 0 1 0 0 0 2 | CAG 4 2 6 6 4 3 | CGG 0 0 0 0 1 0
--------------------------------------------------------------------------------------------------------------
Ile ATT 6 6 3 3 1 5 | Thr ACT 1 3 1 1 2 3 | Asn AAT 1 3 4 4 2 1 | Ser AGT 1 1 1 1 2 0
ATC 4 4 4 4 6 5 | ACC 2 1 2 1 2 2 | AAC 2 3 4 5 5 1 | AGC 2 2 2 2 1 3
ATA 1 1 2 2 0 0 | ACA 1 1 0 0 0 0 | Lys AAA 2 3 3 3 2 2 | Arg AGA 4 5 4 4 6 5
Met ATG 4 6 5 5 2 4 | ACG 0 1 1 1 1 1 | AAG 5 7 5 5 2 6 | AGG 5 6 5 5 5 5
--------------------------------------------------------------------------------------------------------------
Val GTT 6 1 6 6 4 3 | Ala GCT 3 1 1 1 2 1 | Asp GAT 2 3 1 1 2 2 | Gly GGT 2 2 2 2 1 1
GTC 2 3 3 3 2 3 | GCC 5 3 3 4 4 5 | GAC 2 1 2 1 1 1 | GGC 1 1 1 1 4 1
GTA 2 0 1 1 3 2 | GCA 3 3 3 3 2 7 | Glu GAA 2 3 3 3 4 2 | GGA 1 2 2 2 2 2
GTG 2 0 1 1 3 2 | GCG 0 0 0 0 1 0 | GAG 1 2 2 2 0 1 | GGG 1 1 1 1 1 1
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------
Phe TTT 4 3 3 4 3 3 | Ser TCT 0 0 1 2 0 0 | Tyr TAT 1 3 2 0 2 2 | Cys TGT 0 0 0 0 0 0
TTC 0 1 1 1 1 1 | TCC 1 0 0 0 0 0 | TAC 5 4 4 6 7 7 | TGC 0 0 0 0 0 0
Leu TTA 0 0 2 0 1 1 | TCA 0 2 0 1 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
TTG 2 3 5 4 3 4 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 5 5 5 5 3 3
--------------------------------------------------------------------------------------------------------------
Leu CTT 2 4 4 4 3 3 | Pro CCT 1 1 1 1 1 1 | His CAT 2 1 2 1 1 2 | Arg CGT 6 4 6 6 5 4
CTC 1 0 1 0 0 0 | CCC 3 2 0 1 2 2 | CAC 1 1 1 2 2 0 | CGC 3 4 3 3 0 0
CTA 0 1 0 0 1 1 | CCA 4 1 4 3 2 2 | Gln CAA 0 1 1 3 3 4 | CGA 2 0 1 0 1 1
CTG 5 4 2 3 3 3 | CCG 0 0 2 0 1 1 | CAG 5 2 3 4 3 3 | CGG 0 1 2 0 0 0
--------------------------------------------------------------------------------------------------------------
Ile ATT 5 4 4 2 6 5 | Thr ACT 2 2 2 2 2 2 | Asn AAT 0 1 2 1 0 0 | Ser AGT 3 2 3 0 1 1
ATC 4 4 4 5 4 4 | ACC 0 1 2 2 2 1 | AAC 8 5 4 5 5 6 | AGC 1 2 1 3 1 1
ATA 2 2 1 1 2 2 | ACA 1 3 0 1 1 1 | Lys AAA 1 2 4 1 4 4 | Arg AGA 5 4 5 6 2 2
Met ATG 5 4 5 4 4 3 | ACG 1 2 2 1 1 1 | AAG 6 4 3 5 6 6 | AGG 3 4 2 4 2 3
--------------------------------------------------------------------------------------------------------------
Val GTT 2 4 4 5 5 6 | Ala GCT 3 2 3 2 4 4 | Asp GAT 1 2 1 3 4 4 | Gly GGT 2 4 2 1 2 2
GTC 2 1 1 2 1 1 | GCC 4 6 1 6 3 3 | GAC 1 1 3 1 1 1 | GGC 3 1 1 0 1 1
GTA 2 1 1 2 2 2 | GCA 4 7 6 4 1 1 | Glu GAA 3 3 2 3 3 3 | GGA 1 2 2 2 3 2
GTG 2 1 2 3 1 1 | GCG 0 1 0 0 0 0 | GAG 1 1 2 0 1 1 | GGG 0 1 1 2 1 2
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------
Phe TTT 2 | Ser TCT 1 | Tyr TAT 1 | Cys TGT 0
TTC 3 | TCC 0 | TAC 6 | TGC 0
Leu TTA 4 | TCA 1 | *** TAA 0 | *** TGA 0
TTG 3 | TCG 1 | TAG 0 | Trp TGG 4
--------------------------------------------------
Leu CTT 3 | Pro CCT 1 | His CAT 1 | Arg CGT 3
CTC 0 | CCC 1 | CAC 1 | CGC 4
CTA 0 | CCA 4 | Gln CAA 0 | CGA 2
CTG 3 | CCG 1 | CAG 4 | CGG 0
--------------------------------------------------
Ile ATT 4 | Thr ACT 3 | Asn AAT 4 | Ser AGT 2
ATC 2 | ACC 2 | AAC 1 | AGC 2
ATA 2 | ACA 1 | Lys AAA 6 | Arg AGA 5
Met ATG 5 | ACG 2 | AAG 5 | AGG 2
--------------------------------------------------
Val GTT 0 | Ala GCT 3 | Asp GAT 2 | Gly GGT 3
GTC 2 | GCC 3 | GAC 1 | GGC 2
GTA 2 | GCA 4 | Glu GAA 2 | GGA 1
GTG 0 | GCG 1 | GAG 0 | GGG 3
--------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: __1_H._rufescens
position 1: T:0.17910 C:0.18657 A:0.34328 G:0.29104
position 2: T:0.32090 C:0.15672 A:0.34328 G:0.17910
position 3: T:0.27612 C:0.23881 A:0.23134 G:0.25373
Average T:0.25871 C:0.19403 A:0.30597 G:0.24129
#2: __2_H._sorenseni
position 1: T:0.18657 C:0.20149 A:0.35075 G:0.26119
position 2: T:0.30597 C:0.17164 A:0.33582 G:0.18657
position 3: T:0.26119 C:0.24627 A:0.23134 G:0.26119
Average T:0.25124 C:0.20647 A:0.30597 G:0.23632
#3: __3_H._walallensis
position 1: T:0.18045 C:0.18045 A:0.35338 G:0.28571
position 2: T:0.30827 C:0.17293 A:0.32331 G:0.19549
position 3: T:0.25564 C:0.24812 A:0.24060 G:0.25564
Average T:0.24812 C:0.20050 A:0.30576 G:0.24561
#4: __4_H._kamtschatkana
position 1: T:0.18657 C:0.18657 A:0.35821 G:0.26866
position 2: T:0.31343 C:0.15672 A:0.32836 G:0.20149
position 3: T:0.26866 C:0.22388 A:0.22388 G:0.28358
Average T:0.25622 C:0.18905 A:0.30348 G:0.25124
#5: __5_H._sieboldii
position 1: T:0.15789 C:0.21053 A:0.34586 G:0.28571
position 2: T:0.31579 C:0.12782 A:0.36090 G:0.19549
position 3: T:0.28571 C:0.23308 A:0.23308 G:0.24812
Average T:0.25313 C:0.19048 A:0.31328 G:0.24311
#6: __6_H._discus_hannai
position 1: T:0.15789 C:0.19549 A:0.36090 G:0.28571
position 2: T:0.30075 C:0.15038 A:0.33835 G:0.21053
position 3: T:0.29323 C:0.22556 A:0.22556 G:0.25564
Average T:0.25063 C:0.19048 A:0.30827 G:0.25063
#7: __7_H._gigantea
position 1: T:0.15789 C:0.19549 A:0.35338 G:0.29323
position 2: T:0.30075 C:0.14286 A:0.34586 G:0.21053
position 3: T:0.29323 C:0.22556 A:0.22556 G:0.25564
Average T:0.25063 C:0.18797 A:0.30827 G:0.25313
#8: __8_H._corrugata
position 1: T:0.15789 C:0.22556 A:0.33083 G:0.28571
position 2: T:0.32331 C:0.15038 A:0.30827 G:0.21805
position 3: T:0.27068 C:0.24060 A:0.21805 G:0.27068
Average T:0.25063 C:0.20551 A:0.28571 G:0.25815
#9: __9_H._cracherodii
position 1: T:0.16418 C:0.23134 A:0.33582 G:0.26866
position 2: T:0.31343 C:0.12687 A:0.35821 G:0.20149
position 3: T:0.29851 C:0.23134 A:0.21642 G:0.25373
Average T:0.25871 C:0.19652 A:0.30348 G:0.24129
#10: _10_H._fulgens
position 1: T:0.18797 C:0.21053 A:0.35338 G:0.24812
position 2: T:0.30075 C:0.18045 A:0.30827 G:0.21053
position 3: T:0.27820 C:0.24060 A:0.23308 G:0.24812
Average T:0.25564 C:0.21053 A:0.29825 G:0.23559
#11: _11_H._roei
position 1: T:0.19084 C:0.24427 A:0.29008 G:0.27481
position 2: T:0.31298 C:0.15267 A:0.31298 G:0.22137
position 3: T:0.27481 C:0.28244 A:0.17557 G:0.26718
Average T:0.25954 C:0.22646 A:0.25954 G:0.25445
#12: _12_H._scalaris
position 1: T:0.16794 C:0.22901 A:0.31298 G:0.29008
position 2: T:0.32061 C:0.14504 A:0.30534 G:0.22901
position 3: T:0.26718 C:0.28244 A:0.18321 G:0.26718
Average T:0.25191 C:0.21883 A:0.26718 G:0.26209
#13: _13_H._laevigata
position 1: T:0.15267 C:0.26718 A:0.31298 G:0.26718
position 2: T:0.32824 C:0.17557 A:0.27481 G:0.22137
position 3: T:0.29771 C:0.26718 A:0.18321 G:0.25191
Average T:0.25954 C:0.23664 A:0.25700 G:0.24682
#14: _14_H._cyclobates
position 1: T:0.17424 C:0.22727 A:0.40152 G:0.19697
position 2: T:0.28030 C:0.16667 A:0.30303 G:0.25000
position 3: T:0.29545 C:0.26515 A:0.16667 G:0.27273
Average T:0.25000 C:0.21970 A:0.29040 G:0.23990
#15: _15_H._rubra
position 1: T:0.16031 C:0.24427 A:0.35115 G:0.24427
position 2: T:0.32061 C:0.12977 A:0.32061 G:0.22901
position 3: T:0.25954 C:0.28244 A:0.16794 G:0.29008
Average T:0.24682 C:0.21883 A:0.27990 G:0.25445
#16: _16_H._conicopora
position 1: T:0.16031 C:0.24427 A:0.35115 G:0.24427
position 2: T:0.32061 C:0.12977 A:0.32061 G:0.22901
position 3: T:0.25954 C:0.28244 A:0.16794 G:0.29008
Average T:0.24682 C:0.21883 A:0.27990 G:0.25445
#17: _17_H._pustulata
position 1: T:0.18321 C:0.24427 A:0.29771 G:0.27481
position 2: T:0.31298 C:0.16031 A:0.25191 G:0.27481
position 3: T:0.29008 C:0.26718 A:0.20611 G:0.23664
Average T:0.26209 C:0.22392 A:0.25191 G:0.26209
#18: _18_H._midae
position 1: T:0.17557 C:0.23664 A:0.32824 G:0.25954
position 2: T:0.31298 C:0.21374 A:0.24427 G:0.22901
position 3: T:0.29008 C:0.25954 A:0.19084 G:0.25954
Average T:0.25954 C:0.23664 A:0.25445 G:0.24936
#19: _19_H._ovina
position 1: T:0.13740 C:0.26718 A:0.35878 G:0.23664
position 2: T:0.29008 C:0.18321 A:0.26718 G:0.25954
position 3: T:0.25954 C:0.28244 A:0.19084 G:0.26718
Average T:0.22901 C:0.24427 A:0.27226 G:0.25445
#20: _20_H._diversicolor
position 1: T:0.15909 C:0.20455 A:0.34848 G:0.28788
position 2: T:0.28030 C:0.22727 A:0.23485 G:0.25758
position 3: T:0.28030 C:0.25000 A:0.21970 G:0.25000
Average T:0.23990 C:0.22727 A:0.26768 G:0.26515
#21: _21_H._varia
position 1: T:0.17424 C:0.25000 A:0.33333 G:0.24242
position 2: T:0.30303 C:0.18182 A:0.25758 G:0.25758
position 3: T:0.30303 C:0.20455 A:0.21970 G:0.27273
Average T:0.26010 C:0.21212 A:0.27020 G:0.25758
#22: _22_H._australis
position 1: T:0.17293 C:0.23308 A:0.32331 G:0.27068
position 2: T:0.30075 C:0.19549 A:0.26316 G:0.24060
position 3: T:0.25564 C:0.27820 A:0.20301 G:0.26316
Average T:0.24311 C:0.23559 A:0.26316 G:0.25815
#23: _23_H._t.tuberculata
position 1: T:0.16129 C:0.22581 A:0.34677 G:0.26613
position 2: T:0.32258 C:0.16129 A:0.33871 G:0.17742
position 3: T:0.31452 C:0.24194 A:0.20968 G:0.23387
Average T:0.26613 C:0.20968 A:0.29839 G:0.22581
#24: _24_H._t.coccinea
position 1: T:0.16935 C:0.21774 A:0.33871 G:0.27419
position 2: T:0.32258 C:0.15323 A:0.34677 G:0.17742
position 3: T:0.31452 C:0.22581 A:0.20968 G:0.25000
Average T:0.26882 C:0.19892 A:0.29839 G:0.23387
#25: _25_H._iris
position 1: T:0.19847 C:0.21374 A:0.36641 G:0.22137
position 2: T:0.26718 C:0.22137 A:0.25954 G:0.25191
position 3: T:0.25191 C:0.22901 A:0.25954 G:0.25954
Average T:0.23919 C:0.22137 A:0.29517 G:0.24427
Codon usage in genes
--------------------------------------------------------------
Phe TTT 39 48 | Ser TCT 0 10 | Tyr TAT 15 31 | Cys TGT 0 0
TTC 31 23 | TCC 0 10 | TAC 78 70 | TGC 0 0
Leu TTA 20 2 | TCA 0 7 | *** TAA 0 0 | *** TGA 0 0
TTG 53 16 | TCG 2 3 | TAG 0 0 | Trp TGG 65 37
--------------------------------------------------------------
Leu CTT 48 17 | Pro CCT 8 18 | His CAT 2 42 | Arg CGT 0 97
CTC 4 11 | CCC 1 27 | CAC 0 43 | CGC 0 60
CTA 2 2 | CCA 16 65 | Gln CAA 1 31 | CGA 1 21
CTG 80 16 | CCG 0 12 | CAG 24 71 | CGG 0 13
--------------------------------------------------------------
Ile ATT 52 44 | Thr ACT 1 42 | Asn AAT 30 44 | Ser AGT 0 20
ATC 91 3 | ACC 4 35 | AAC 13 80 | AGC 0 35
ATA 26 5 | ACA 2 16 | Lys AAA 0 78 | Arg AGA 18 120
Met ATG 100 29 | ACG 14 11 | AAG 26 111 | AGG 7 68
--------------------------------------------------------------
Val GTT 44 84 | Ala GCT 2 58 | Asp GAT 1 74 | Gly GGT 26 23
GTC 20 35 | GCC 0 73 | GAC 24 11 | GGC 24 17
GTA 15 22 | GCA 22 65 | Glu GAA 24 57 | GGA 34 17
GTG 5 26 | GCG 8 12 | GAG 0 26 | GGG 15 8
--------------------------------------------------------------
Codon position x base (3x4) table for each gene.
Gene #1
position 1: T:0.26626 C:0.16432 A:0.33743 G:0.23199
position 2: T:0.55360 C:0.07030 A:0.20914 G:0.16696
position 3: T:0.23550 C:0.25483 A:0.15905 G:0.35062
Average T:0.35179 C:0.16315 A:0.23521 G:0.24985
Gene #2
position 1: T:0.11942 C:0.25372 A:0.34433 G:0.28253
position 2: T:0.17797 C:0.21561 A:0.35734 G:0.24907
position 3: T:0.30297 C:0.24768 A:0.23606 G:0.21329
Average T:0.20012 C:0.23900 A:0.31258 G:0.24830
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 87 | Ser S TCT 10 | Tyr Y TAT 46 | Cys C TGT 0
TTC 54 | TCC 10 | TAC 148 | TGC 0
Leu L TTA 22 | TCA 7 | *** * TAA 0 | *** * TGA 0
TTG 69 | TCG 5 | TAG 0 | Trp W TGG 102
------------------------------------------------------------------------------
Leu L CTT 65 | Pro P CCT 26 | His H CAT 44 | Arg R CGT 97
CTC 15 | CCC 28 | CAC 43 | CGC 60
CTA 4 | CCA 81 | Gln Q CAA 32 | CGA 22
CTG 96 | CCG 12 | CAG 95 | CGG 13
------------------------------------------------------------------------------
Ile I ATT 96 | Thr T ACT 43 | Asn N AAT 74 | Ser S AGT 20
ATC 94 | ACC 39 | AAC 93 | AGC 35
ATA 31 | ACA 18 | Lys K AAA 78 | Arg R AGA 138
Met M ATG 129 | ACG 25 | AAG 137 | AGG 75
------------------------------------------------------------------------------
Val V GTT 128 | Ala A GCT 60 | Asp D GAT 75 | Gly G GGT 49
GTC 55 | GCC 73 | GAC 35 | GGC 41
GTA 37 | GCA 87 | Glu E GAA 81 | GGA 51
GTG 31 | GCG 20 | GAG 26 | GGG 23
------------------------------------------------------------------------------
(Ambiguity data are not used in the counts.)
Codon position x base (3x4) table, overall
position 1: T:0.17021 C:0.22280 A:0.34195 G:0.26505
position 2: T:0.30790 C:0.16535 A:0.30608 G:0.22067
position 3: T:0.27964 C:0.25015 A:0.20942 G:0.26079
Average T:0.25258 C:0.21277 A:0.28582 G:0.24883
Nei & Gojobori 1986. dN/dS (dN, dS)
(Pairwise deletion)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)
__1_H._rufescens
__2_H._sorenseni 3.4195 (0.0581 0.0170)
__3_H._walallensis 4.7194 (0.0936 0.0198) 1.5215 (0.0563 0.0370)
__4_H._kamtschatkana 3.7286 (0.1078 0.0289) 2.4431 (0.0844 0.0346) 2.6160 (0.1290 0.0493)
__5_H._sieboldii 1.7428 (0.1222 0.0701) 1.4909 (0.1193 0.0800) 1.4940 (0.1321 0.0884) 1.5480 (0.1489 0.0962)
__6_H._discus_hannai 2.4504 (0.1803 0.0736) 1.9797 (0.1651 0.0834) 1.5555 (0.1526 0.0981) 2.3180 (0.2007 0.0866) 1.1844 (0.0565 0.0477)
__7_H._gigantea 2.6416 (0.1781 0.0674) 2.1103 (0.1631 0.0773) 1.6389 (0.1506 0.0919) 2.4708 (0.1985 0.0803) 1.3148 (0.0547 0.0416)-1.0000 (0.0064 0.0000)
__8_H._corrugata 1.3495 (0.1426 0.1056) 1.3523 (0.1332 0.0985) 1.4124 (0.1568 0.1110) 1.8378 (0.1773 0.0965) 2.0360 (0.1284 0.0630) 3.5019 (0.1762 0.0503) 3.9203 (0.1741 0.0444)
__9_H._cracherodii 1.9850 (0.2205 0.1111) 1.8431 (0.2111 0.1145) 1.7378 (0.2257 0.1299) 1.9105 (0.2642 0.1383) 2.8137 (0.1504 0.0535) 2.0571 (0.1728 0.0840) 2.2458 (0.1748 0.0778) 1.3398 (0.1329 0.0992)
_10_H._fulgens 1.1562 (0.2407 0.2082) 1.1907 (0.2458 0.2065) 1.0055 (0.2370 0.2357) 1.0681 (0.2367 0.2216) 1.6087 (0.2483 0.1544) 1.4175 (0.2395 0.1689) 1.3622 (0.2305 0.1692) 1.5551 (0.2328 0.1497) 1.5698 (0.2704 0.1722)
_11_H._roei 0.4688 (0.3509 0.7484) 0.4467 (0.3346 0.7490) 0.4292 (0.3422 0.7974) 0.5410 (0.3805 0.7032) 0.4423 (0.3061 0.6920) 0.4335 (0.3441 0.7937) 0.4505 (0.3439 0.7633) 0.3866 (0.3071 0.7943) 0.4791 (0.3415 0.7129) 0.4385 (0.3287 0.7496)
_12_H._scalaris 0.4611 (0.3841 0.8330) 0.4215 (0.3511 0.8330) 0.3933 (0.3524 0.8960) 0.5226 (0.4094 0.7835) 0.4108 (0.3205 0.7802) 0.4063 (0.3604 0.8869) 0.4222 (0.3602 0.8531) 0.3392 (0.2985 0.8801) 0.3931 (0.3378 0.8594) 0.5200 (0.4035 0.7760) 1.8859 (0.1194 0.0633)
_13_H._laevigata 0.4589 (0.3830 0.8346) 0.4194 (0.3500 0.8346) 0.3798 (0.3408 0.8973) 0.5272 (0.4141 0.7854) 0.3487 (0.3058 0.8768) 0.3753 (0.3562 0.9490) 0.3900 (0.3560 0.9127) 0.3593 (0.3244 0.9028) 0.4457 (0.3683 0.8262) 0.4776 (0.3779 0.7911) 1.5424 (0.1095 0.0710) 1.8705 (0.0935 0.0500)
_14_H._cyclobates 0.6729 (0.4542 0.6750) 0.6917 (0.4302 0.6219) 0.5795 (0.4333 0.7478) 0.7896 (0.5003 0.6335) 0.6439 (0.4412 0.6852) 0.6261 (0.4787 0.7646) 0.6591 (0.4846 0.7352) 0.6007 (0.4153 0.6914) 0.7570 (0.4669 0.6168) 0.6911 (0.4475 0.6475) 2.2092 (0.2333 0.1056) 2.0852 (0.2592 0.1243) 1.8398 (0.2431 0.1322)
_15_H._rubra 0.5483 (0.3858 0.7037) 0.5299 (0.3582 0.6760) 0.4534 (0.3438 0.7582) 0.6308 (0.4168 0.6608) 0.4783 (0.3312 0.6925) 0.4321 (0.3556 0.8231) 0.4491 (0.3554 0.7914) 0.4471 (0.3274 0.7323) 0.5774 (0.3828 0.6630) 0.6172 (0.4010 0.6496) 1.3592 (0.1194 0.0878) 1.6838 (0.1606 0.0954) 1.0141 (0.1337 0.1319) 1.6679 (0.1808 0.1084)
_16_H._conicopora 0.5483 (0.3858 0.7037) 0.5299 (0.3582 0.6760) 0.4534 (0.3438 0.7582) 0.6308 (0.4168 0.6608) 0.4783 (0.3312 0.6925) 0.4449 (0.3662 0.8231) 0.4624 (0.3660 0.7914) 0.4471 (0.3274 0.7323) 0.5611 (0.3720 0.6630) 0.6172 (0.4010 0.6496) 1.3592 (0.1194 0.0878) 1.6838 (0.1606 0.0954) 1.0141 (0.1337 0.1319) 1.6319 (0.1732 0.1061)-1.0000 (0.0065 0.0000)
_17_H._pustulata 0.5767 (0.4532 0.7859) 0.5513 (0.4084 0.7409) 0.4820 (0.4027 0.8354) 0.5691 (0.4475 0.7863) 0.4795 (0.3872 0.8073) 0.4940 (0.3895 0.7885) 0.5126 (0.3893 0.7594) 0.4543 (0.3562 0.7841) 0.5434 (0.4117 0.7576) 0.4726 (0.3755 0.7945) 0.3643 (0.1636 0.4491) 0.4887 (0.2067 0.4229) 0.5081 (0.2000 0.3935) 0.5688 (0.2656 0.4669) 0.3054 (0.1411 0.4622) 0.3140 (0.1451 0.4622)
_18_H._midae 0.4268 (0.3710 0.8692) 0.4297 (0.3515 0.8180) 0.3740 (0.3422 0.9150) 0.4280 (0.3961 0.9253) 0.4124 (0.3195 0.7747) 0.3563 (0.3240 0.9092) 0.3653 (0.3263 0.8932) 0.3089 (0.2787 0.9021) 0.3912 (0.2961 0.7571) 0.3423 (0.2801 0.8182) 0.6126 (0.1615 0.2636) 0.7585 (0.1993 0.2627) 0.6802 (0.1995 0.2932) 1.0695 (0.3000 0.2805) 0.7598 (0.2189 0.2881) 0.7598 (0.2189 0.2881) 0.4660 (0.2146 0.4606)
_19_H._ovina 0.5785 (0.4062 0.7021) 0.5532 (0.3686 0.6663) 0.4669 (0.3560 0.7625) 0.5247 (0.3760 0.7166) 0.6057 (0.3908 0.6452) 0.5129 (0.4025 0.7847) 0.5325 (0.4022 0.7554) 0.4737 (0.3458 0.7299) 0.7311 (0.4135 0.5655) 0.5271 (0.3518 0.6674) 0.6318 (0.1718 0.2720) 0.6535 (0.2130 0.3260) 0.6097 (0.1934 0.3171) 0.7482 (0.2279 0.3046) 0.5279 (0.1771 0.3355) 0.5279 (0.1771 0.3355) 0.4104 (0.1917 0.4672) 0.6510 (0.2647 0.4066)
_20_H._diversicolor 0.3931 (0.3500 0.8904) 0.3886 (0.3260 0.8388) 0.3716 (0.3364 0.9054) 0.4162 (0.3636 0.8735) 0.4809 (0.3827 0.7957) 0.4484 (0.3750 0.8363) 0.4786 (0.3857 0.8058) 0.4040 (0.3403 0.8423) 0.5117 (0.4170 0.8148) 0.5416 (0.3890 0.7181) 0.6281 (0.2042 0.3252) 0.6238 (0.2287 0.3666) 0.6009 (0.2323 0.3866) 1.0485 (0.3347 0.3192) 0.8982 (0.2736 0.3046) 0.9296 (0.2832 0.3046) 0.4246 (0.2469 0.5815) 0.3835 (0.2123 0.5534) 0.5408 (0.1886 0.3488)
_21_H._varia 0.5062 (0.4048 0.7995) 0.4615 (0.3666 0.7945) 0.4295 (0.3518 0.8192) 0.4682 (0.3848 0.8219) 0.5212 (0.3841 0.7369) 0.4260 (0.3836 0.9005) 0.4423 (0.3834 0.8668) 0.3999 (0.3299 0.8249) 0.5554 (0.4059 0.7309) 0.4937 (0.3495 0.7080) 0.4582 (0.2035 0.4441) 0.4871 (0.2504 0.5141) 0.4873 (0.2565 0.5265) 0.5532 (0.3278 0.5925) 0.4498 (0.2452 0.5452) 0.4332 (0.2362 0.5452) 0.4019 (0.2164 0.5384) 0.5142 (0.2537 0.4933) 0.4742 (0.1379 0.2907) 0.3222 (0.1843 0.5720)
_22_H._australis 0.5454 (0.3717 0.6816) 0.4901 (0.3346 0.6826) 0.4320 (0.3122 0.7227) 0.5713 (0.3765 0.6590) 0.5356 (0.3292 0.6147) 0.4704 (0.3208 0.6820) 0.5035 (0.3306 0.6565) 0.5174 (0.3283 0.6346) 0.6297 (0.3621 0.5751) 0.5628 (0.3396 0.6035) 0.4530 (0.1468 0.3241) 0.5904 (0.1887 0.3196) 0.4921 (0.1641 0.3334) 0.7647 (0.2746 0.3590) 0.5758 (0.1877 0.3260) 0.6018 (0.1962 0.3260) 0.5015 (0.2078 0.4143) 0.5357 (0.2124 0.3964) 0.4351 (0.1846 0.4243) 0.3055 (0.1500 0.4909) 0.3666 (0.2198 0.5995)
_23_H._t.tuberculata 0.5584 (0.3912 0.7005) 0.6095 (0.4000 0.6563) 0.5653 (0.4011 0.7095) 0.5927 (0.4432 0.7477) 0.5870 (0.4014 0.6838) 0.6151 (0.4240 0.6894) 0.6222 (0.4207 0.6762) 0.5437 (0.3795 0.6981) 0.6450 (0.4058 0.6291) 0.4934 (0.4093 0.8294) 0.7112 (0.2270 0.3192) 0.7660 (0.2757 0.3599) 0.8320 (0.2698 0.3243) 0.7634 (0.2768 0.3626) 0.5316 (0.2095 0.3942) 0.5134 (0.2041 0.3976) 0.8275 (0.1866 0.2255) 0.7358 (0.2760 0.3752) 0.8350 (0.2854 0.3418) 0.5825 (0.3309 0.5681) 0.5974 (0.3142 0.5260) 0.7356 (0.2746 0.3732)
_24_H._t.coccinea 0.5400 (0.3835 0.7101) 0.6070 (0.3951 0.6510) 0.5012 (0.3846 0.7674) 0.6445 (0.4381 0.6796) 0.5761 (0.3908 0.6783) 0.6312 (0.4130 0.6544) 0.6385 (0.4098 0.6417) 0.6078 (0.3777 0.6214) 0.6119 (0.4004 0.6544) 0.4730 (0.4094 0.8655) 0.6865 (0.2319 0.3378) 0.7537 (0.2860 0.3794) 0.7873 (0.2698 0.3427) 0.6993 (0.2819 0.4032) 0.5276 (0.2189 0.4149) 0.5100 (0.2134 0.4185) 0.8896 (0.1935 0.2176) 0.7640 (0.2864 0.3749) 0.8654 (0.3039 0.3511) 0.6412 (0.3561 0.5554) 0.6486 (0.3333 0.5138) 0.6456 (0.2797 0.4332) 1.3231 (0.0319 0.0241)
_25_H._iris 0.9376 (0.4857 0.5180) 0.8452 (0.4552 0.5386) 0.9136 (0.4591 0.5025) 0.8482 (0.4745 0.5594) 1.0104 (0.4652 0.4604) 1.0001 (0.4930 0.4929) 1.0262 (0.4959 0.4832) 0.8870 (0.4466 0.5035) 0.9604 (0.4982 0.5188) 0.7013 (0.4302 0.6134) 0.6136 (0.3024 0.4927) 0.6247 (0.3446 0.5517) 0.6046 (0.3413 0.5645) 0.7647 (0.3761 0.4918) 0.7035 (0.3287 0.4673) 0.6817 (0.3185 0.4673) 0.4765 (0.3332 0.6992) 0.3764 (0.2941 0.7814) 0.3831 (0.2558 0.6677) 0.3292 (0.2647 0.8043) 0.3849 (0.2932 0.7616) 0.4867 (0.3067 0.6301) 0.7794 (0.3927 0.5039) 0.7453 (0.4018 0.5390)
Gene 1 ls: 46 npatt: 44
Nei & Gojobori 1986. dN/dS (dN, dS)
(Pairwise deletion)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)
__1_H._rufescens
__2_H._sorenseni -1.0000 (0.0188 0.0000)
__3_H._walallensis -1.0000 (0.0380 0.0000)-1.0000 (0.0380 0.0000)
__4_H._kamtschatkana-1.0000 (0.0479 0.0000)-1.0000 (0.0284 0.0000)-1.0000 (0.0679 0.0000)
__5_H._sieboldii -1.0000 (0.0479 0.0000)-1.0000 (0.0479 0.0000)-1.0000 (0.0479 0.0000)-1.0000 (0.0783 0.0000)
__6_H._discus_hannai-1.0000 (0.0580 0.0000)-1.0000 (0.0580 0.0000)-1.0000 (0.0381 0.0000)-1.0000 (0.0889 0.0000)-1.0000 (0.0094 0.0000)
__7_H._gigantea -1.0000 (0.0580 0.0000)-1.0000 (0.0580 0.0000)-1.0000 (0.0381 0.0000)-1.0000 (0.0889 0.0000)-1.0000 (0.0094 0.0000)-1.0000 (0.0000 0.0000)
__8_H._corrugata -1.0000 (0.0284 0.0000)-1.0000 (0.0284 0.0000)-1.0000 (0.0578 0.0000)-1.0000 (0.0579 0.0000)-1.0000 (0.0480 0.0000)-1.0000 (0.0580 0.0000)-1.0000 (0.0580 0.0000)
__9_H._cracherodii 1.0333 (0.0529 0.0512) 1.0333 (0.0529 0.0512) 1.1289 (0.0782 0.0692) 1.6349 (0.0835 0.0511) 0.7001 (0.0480 0.0686) 0.8522 (0.0581 0.0682) 0.8522 (0.0581 0.0682) 0.2726 (0.0188 0.0690)
_10_H._fulgens 0.5244 (0.0778 0.1483) 0.6645 (0.0986 0.1483) 0.5918 (0.0880 0.1487) 0.8853 (0.1309 0.1479) 0.5294 (0.0779 0.1472) 0.4639 (0.0679 0.1463) 0.4639 (0.0679 0.1463) 0.4563 (0.0676 0.1482) 0.2898 (0.0677 0.2337)
_11_H._roei 0.2146 (0.1120 0.5218) 0.2146 (0.1120 0.5218) 0.1904 (0.1064 0.5591) 0.3207 (0.1458 0.4546) 0.1552 (0.0853 0.5493) 0.1766 (0.0961 0.5445) 0.1766 (0.0961 0.5445) 0.2122 (0.1176 0.5541) 0.2439 (0.1178 0.4828) 0.1753 (0.1282 0.7312)
_12_H._scalaris 0.2761 (0.1236 0.4476) 0.2761 (0.1236 0.4476) 0.2453 (0.1179 0.4806) 0.4080 (0.1581 0.3874) 0.2038 (0.0964 0.4727) 0.2292 (0.1075 0.4689) 0.2292 (0.1075 0.4689) 0.2713 (0.1293 0.4766) 0.3134 (0.1295 0.4132) 0.2404 (0.1515 0.6304) 1.9797 (0.0693 0.0350)
_13_H._laevigata 0.2320 (0.1348 0.5812) 0.2320 (0.1348 0.5812) 0.1720 (0.1069 0.6213) 0.3334 (0.1699 0.5095) 0.1758 (0.1073 0.6100) 0.1961 (0.1185 0.6046) 0.1961 (0.1185 0.6046) 0.2286 (0.1407 0.6156) 0.2900 (0.1467 0.5057) 0.2020 (0.1632 0.8079) 1.9797 (0.0693 0.0350) 1.1292 (0.0390 0.0345)
_14_H._cyclobates 0.3925 (0.1647 0.4196) 0.3925 (0.1647 0.4196) 0.3771 (0.1704 0.4520) 0.5575 (0.2010 0.3605) 0.3322 (0.1477 0.4446) 0.3619 (0.1596 0.4410) 0.3619 (0.1596 0.4410) 0.3547 (0.1590 0.4483) 0.4613 (0.1651 0.3579) 0.2838 (0.1700 0.5988) 2.5082 (0.0898 0.0358)14.2295 (0.1647 0.0116) 1.5262 (0.1396 0.0915)
_15_H._rubra 0.3049 (0.1425 0.4674) 0.3049 (0.1425 0.4674) 0.2279 (0.1143 0.5013) 0.4386 (0.1779 0.4057) 0.2075 (0.1091 0.5259) 0.2310 (0.1205 0.5215) 0.2310 (0.1205 0.5215) 0.2986 (0.1484 0.4972) 0.3441 (0.1487 0.4320) 0.2430 (0.1594 0.6558) 0.4039 (0.0289 0.0716) 2.1143 (0.0979 0.0463) 0.5835 (0.0748 0.1283) 5.4883 (0.0955 0.0174)
_16_H._conicopora 0.3049 (0.1425 0.4674) 0.3049 (0.1425 0.4674) 0.2279 (0.1143 0.5013) 0.4386 (0.1779 0.4057) 0.2075 (0.1091 0.5259) 0.2310 (0.1205 0.5215) 0.2310 (0.1205 0.5215) 0.2986 (0.1484 0.4972) 0.3441 (0.1487 0.4320) 0.2430 (0.1594 0.6558) 0.4039 (0.0289 0.0716) 2.1143 (0.0979 0.0463) 0.5835 (0.0748 0.1283) 5.4883 (0.0955 0.0174)-1.0000 (0.0000 0.0000)
_17_H._pustulata 0.2923 (0.1469 0.5024) 0.2923 (0.1469 0.5024) 0.2682 (0.1353 0.5043) 0.4165 (0.1826 0.4385) 0.2737 (0.1358 0.4960) 0.2533 (0.1246 0.4919) 0.2533 (0.1246 0.4919) 0.3173 (0.1587 0.5001) 0.3199 (0.1589 0.4969) 0.2225 (0.1463 0.6576) 0.1257 (0.0490 0.3898) 0.2816 (0.1240 0.4405) 0.2816 (0.1240 0.4405) 0.2164 (0.1121 0.5183) 0.1185 (0.0595 0.5020) 0.1185 (0.0595 0.5020)
_18_H._midae 0.2256 (0.1342 0.5949) 0.2256 (0.1342 0.5949) 0.2058 (0.1229 0.5973) 0.3246 (0.1691 0.5209) 0.1728 (0.1013 0.5865) 0.1935 (0.1125 0.5812) 0.1935 (0.1125 0.5812) 0.2463 (0.1458 0.5918) 0.2825 (0.1460 0.5168) 0.2859 (0.1624 0.5682) 0.1991 (0.0486 0.2442) 0.5198 (0.1010 0.1944) 0.3761 (0.0903 0.2401) 0.6133 (0.1222 0.1992) 0.2044 (0.0539 0.2636) 0.2044 (0.0539 0.2636) 0.1557 (0.0800 0.5139)
_19_H._ovina 0.2919 (0.1404 0.4811) 0.2919 (0.1404 0.4811) 0.2391 (0.1233 0.5158) 0.2695 (0.1292 0.4793) 0.2441 (0.1238 0.5071) 0.2244 (0.1129 0.5029) 0.2244 (0.1129 0.5029) 0.2637 (0.1348 0.5114) 0.3495 (0.1350 0.3864) 0.1698 (0.1010 0.5949) 0.1334 (0.0797 0.5973) 0.3067 (0.1577 0.5143) 0.2440 (0.1519 0.6225) 0.3330 (0.1338 0.4019) 0.2189 (0.1124 0.5133) 0.2189 (0.1124 0.5133) 0.2014 (0.1018 0.5053) 0.1487 (0.1009 0.6790)
_20_H._diversicolor 0.0976 (0.0804 0.8230) 0.1106 (0.0910 0.8230) 0.1540 (0.1128 0.7325) 0.1709 (0.1241 0.7261) 0.1576 (0.1132 0.7183) 0.1751 (0.1246 0.7114) 0.1751 (0.1246 0.7114) 0.1406 (0.1020 0.7253) 0.1532 (0.1243 0.8115) 0.1416 (0.1348 0.9522) 0.1518 (0.0592 0.3901) 0.4106 (0.1353 0.3295) 0.2813 (0.1240 0.4408) 0.3314 (0.1121 0.3383) 0.3263 (0.0911 0.2791) 0.3263 (0.0911 0.2791) 0.1441 (0.0914 0.6342) 0.1049 (0.0695 0.6624) 0.1239 (0.0909 0.7341)
_21_H._varia 0.2292 (0.1346 0.5872) 0.2292 (0.1346 0.5872) 0.2090 (0.1232 0.5895) 0.2899 (0.1695 0.5848) 0.2136 (0.1237 0.5790) 0.1965 (0.1127 0.5738) 0.1965 (0.1127 0.5738) 0.2502 (0.1461 0.5842) 0.2867 (0.1464 0.5105) 0.2092 (0.1173 0.5609) 0.0631 (0.0487 0.7720) 0.1852 (0.1233 0.6659) 0.1317 (0.1122 0.8523) 0.1979 (0.1281 0.6473) 0.1064 (0.0799 0.7516) 0.1064 (0.0799 0.7516) 0.1169 (0.0593 0.5076) 0.1149 (0.0691 0.6016) 0.0986 (0.0389 0.3942) 0.0739 (0.0697 0.9434)
_22_H._australis 0.2384 (0.1202 0.5043) 0.2384 (0.1202 0.5043) 0.2125 (0.1147 0.5397) 0.3492 (0.1537 0.4401) 0.1564 (0.0833 0.5326) 0.1778 (0.0939 0.5281) 0.1778 (0.0939 0.5281) 0.2138 (0.1148 0.5371) 0.2453 (0.1150 0.4688) 0.1774 (0.1251 0.7052) 0.0000 (0.0000 0.4587) 0.2070 (0.0695 0.3358) 0.1779 (0.0695 0.3907) 0.2273 (0.0847 0.3729) 0.0865 (0.0290 0.3353) 0.0865 (0.0290 0.3353) 0.1279 (0.0492 0.3844) 0.1223 (0.0488 0.3987) 0.1360 (0.0799 0.5876) 0.1034 (0.0594 0.5744) 0.0570 (0.0489 0.8576)
_23_H._t.tuberculata 0.2689 (0.1473 0.5478) 0.2689 (0.1473 0.5478) 0.2474 (0.1361 0.5499) 0.3798 (0.1819 0.4790) 0.3143 (0.1705 0.5424) 0.2961 (0.1592 0.5377) 0.2961 (0.1592 0.5377) 0.3110 (0.1701 0.5471) 0.4484 (0.2000 0.4460) 0.2217 (0.1810 0.8160) 0.1952 (0.0793 0.4063) 0.3416 (0.1570 0.4595) 0.2917 (0.1341 0.4595) 0.1848 (0.1003 0.5428) 0.1511 (0.0902 0.5973) 0.1511 (0.0902 0.5973) 0.2432 (0.0695 0.2856) 0.1442 (0.1005 0.6966) 0.2980 (0.1283 0.4305) 0.1062 (0.0905 0.8523) 0.1713 (0.0795 0.4640) 0.1694 (0.0878 0.5183)
_24_H._t.coccinea 0.2456 (0.1482 0.6034) 0.2456 (0.1482 0.6034) 0.2259 (0.1368 0.6058) 0.3448 (0.1830 0.5307) 0.2676 (0.1599 0.5974) 0.2512 (0.1487 0.5921) 0.2512 (0.1487 0.5921) 0.2840 (0.1712 0.6027) 0.3813 (0.1891 0.4960) 0.1911 (0.1703 0.8913) 0.1750 (0.0693 0.3959) 0.3269 (0.1463 0.4476) 0.2761 (0.1236 0.4476) 0.2119 (0.1117 0.5274) 0.1381 (0.0801 0.5801) 0.1381 (0.0801 0.5801) 0.2131 (0.0595 0.2791) 0.1339 (0.0903 0.6747) 0.2450 (0.1179 0.4811) 0.1106 (0.0910 0.8230) 0.1538 (0.0695 0.4517) 0.1546 (0.0780 0.5043)-1.0000 (0.0187 0.0000)
_25_H._iris 1.0119 (0.1938 0.1915) 0.8784 (0.1876 0.2136) 0.8823 (0.1695 0.1921) 1.0579 (0.2253 0.2130) 1.0257 (0.1943 0.1895) 0.9695 (0.1825 0.1882) 0.9695 (0.1825 0.1882) 0.9993 (0.2126 0.2128) 0.7790 (0.2193 0.2815) 0.5313 (0.1809 0.3405) 0.2489 (0.1064 0.4275) 0.4650 (0.1815 0.3904) 0.3070 (0.1578 0.5139) 0.5937 (0.2047 0.3448) 0.2816 (0.1179 0.4187) 0.2816 (0.1179 0.4187) 0.2161 (0.1239 0.5733) 0.2338 (0.1229 0.5254) 0.2062 (0.1289 0.6252) 0.2000 (0.1467 0.7333) 0.1532 (0.0904 0.5902) 0.1707 (0.1067 0.6252) 0.3293 (0.1627 0.4940) 0.2847 (0.1462 0.5135)
TREE # 1: ((10, (((4, (1, (2, 3))), (5, (6, 7))), (8, 9))), 25, ((17, (24, 23)), (22, ((18, ((11, (12, 13)), (14, (15, 16)))), ((19, 21), 20))))); MP score: -1
lnL(ntime: 47 np: 49): -937.847082 +0.000000
26..27 27..10 27..28 28..29 29..30 30..4 30..31 31..1 31..32 32..2 32..3 29..33 33..5 33..34 34..6 34..7 28..35 35..8 35..9 26..25 26..36 36..37 37..17 37..38 38..24 38..23 36..39 39..22 39..40 40..41 41..18 41..42 42..43 43..11 43..44 44..12 44..13 42..45 45..14 45..46 46..15 46..16 40..47 47..48 48..19 48..21 47..20
0.319242 0.169635 0.077453 0.032556 0.067922 0.070665 0.000004 0.045815 0.000004 0.000004 0.092850 0.063369 0.000004 0.022585 0.000004 0.000004 0.000004 0.022988 0.069929 0.343072 0.111516 0.081055 0.113022 0.236612 0.000004 0.045174 0.047198 0.129516 0.041196 0.052590 0.189960 0.058773 0.000004 0.021586 0.135299 0.042722 0.076885 0.032680 0.198011 0.061005 0.000004 0.000004 0.032071 0.203594 0.224570 0.125572 0.297645 1.961699 0.451716
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 3.95638
((10: 0.169635, (((4: 0.070665, (1: 0.045815, (2: 0.000004, 3: 0.092850): 0.000004): 0.000004): 0.067922, (5: 0.000004, (6: 0.000004, 7: 0.000004): 0.022585): 0.063369): 0.032556, (8: 0.022988, 9: 0.069929): 0.000004): 0.077453): 0.319242, 25: 0.343072, ((17: 0.113022, (24: 0.000004, 23: 0.045174): 0.236612): 0.081055, (22: 0.129516, ((18: 0.189960, ((11: 0.021586, (12: 0.042722, 13: 0.076885): 0.135299): 0.000004, (14: 0.198011, (15: 0.000004, 16: 0.000004): 0.061005): 0.032680): 0.058773): 0.052590, ((19: 0.224570, 21: 0.125572): 0.203594, 20: 0.297645): 0.032071): 0.041196): 0.047198): 0.111516);
((_10_H._fulgens: 0.169635, (((__4_H._kamtschatkana: 0.070665, (__1_H._rufescens: 0.045815, (__2_H._sorenseni: 0.000004, __3_H._walallensis: 0.092850): 0.000004): 0.000004): 0.067922, (__5_H._sieboldii: 0.000004, (__6_H._discus_hannai: 0.000004, __7_H._gigantea: 0.000004): 0.022585): 0.063369): 0.032556, (__8_H._corrugata: 0.022988, __9_H._cracherodii: 0.069929): 0.000004): 0.077453): 0.319242, _25_H._iris: 0.343072, ((_17_H._pustulata: 0.113022, (_24_H._t.coccinea: 0.000004, _23_H._t.tuberculata: 0.045174): 0.236612): 0.081055, (_22_H._australis: 0.129516, ((_18_H._midae: 0.189960, ((_11_H._roei: 0.021586, (_12_H._scalaris: 0.042722, _13_H._laevigata: 0.076885): 0.135299): 0.000004, (_14_H._cyclobates: 0.198011, (_15_H._rubra: 0.000004, _16_H._conicopora: 0.000004): 0.061005): 0.032680): 0.058773): 0.052590, ((_19_H._ovina: 0.224570, _21_H._varia: 0.125572): 0.203594, _20_H._diversicolor: 0.297645): 0.032071): 0.041196): 0.047198): 0.111516);
Detailed output identifying parameters
kappa (ts/tv) = 1.96170
omega (dN/dS) = 0.45172
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
26..27 0.319 100.4 37.6 0.4517 0.0800 0.1771 8.0 6.7
27..10 0.170 100.4 37.6 0.4517 0.0425 0.0941 4.3 3.5
27..28 0.077 100.4 37.6 0.4517 0.0194 0.0430 1.9 1.6
28..29 0.033 100.4 37.6 0.4517 0.0082 0.0181 0.8 0.7
29..30 0.068 100.4 37.6 0.4517 0.0170 0.0377 1.7 1.4
30..4 0.071 100.4 37.6 0.4517 0.0177 0.0392 1.8 1.5
30..31 0.000 100.4 37.6 0.4517 0.0000 0.0000 0.0 0.0
31..1 0.046 100.4 37.6 0.4517 0.0115 0.0254 1.2 1.0
31..32 0.000 100.4 37.6 0.4517 0.0000 0.0000 0.0 0.0
32..2 0.000 100.4 37.6 0.4517 0.0000 0.0000 0.0 0.0
32..3 0.093 100.4 37.6 0.4517 0.0233 0.0515 2.3 1.9
29..33 0.063 100.4 37.6 0.4517 0.0159 0.0351 1.6 1.3
33..5 0.000 100.4 37.6 0.4517 0.0000 0.0000 0.0 0.0
33..34 0.023 100.4 37.6 0.4517 0.0057 0.0125 0.6 0.5
34..6 0.000 100.4 37.6 0.4517 0.0000 0.0000 0.0 0.0
34..7 0.000 100.4 37.6 0.4517 0.0000 0.0000 0.0 0.0
28..35 0.000 100.4 37.6 0.4517 0.0000 0.0000 0.0 0.0
35..8 0.023 100.4 37.6 0.4517 0.0058 0.0128 0.6 0.5
35..9 0.070 100.4 37.6 0.4517 0.0175 0.0388 1.8 1.5
26..25 0.343 100.4 37.6 0.4517 0.0860 0.1903 8.6 7.1
26..36 0.112 100.4 37.6 0.4517 0.0279 0.0619 2.8 2.3
36..37 0.081 100.4 37.6 0.4517 0.0203 0.0450 2.0 1.7
37..17 0.113 100.4 37.6 0.4517 0.0283 0.0627 2.8 2.4
37..38 0.237 100.4 37.6 0.4517 0.0593 0.1312 6.0 4.9
38..24 0.000 100.4 37.6 0.4517 0.0000 0.0000 0.0 0.0
38..23 0.045 100.4 37.6 0.4517 0.0113 0.0251 1.1 0.9
36..39 0.047 100.4 37.6 0.4517 0.0118 0.0262 1.2 1.0
39..22 0.130 100.4 37.6 0.4517 0.0325 0.0718 3.3 2.7
39..40 0.041 100.4 37.6 0.4517 0.0103 0.0228 1.0 0.9
40..41 0.053 100.4 37.6 0.4517 0.0132 0.0292 1.3 1.1
41..18 0.190 100.4 37.6 0.4517 0.0476 0.1054 4.8 4.0
41..42 0.059 100.4 37.6 0.4517 0.0147 0.0326 1.5 1.2
42..43 0.000 100.4 37.6 0.4517 0.0000 0.0000 0.0 0.0
43..11 0.022 100.4 37.6 0.4517 0.0054 0.0120 0.5 0.4
43..44 0.135 100.4 37.6 0.4517 0.0339 0.0750 3.4 2.8
44..12 0.043 100.4 37.6 0.4517 0.0107 0.0237 1.1 0.9
44..13 0.077 100.4 37.6 0.4517 0.0193 0.0426 1.9 1.6
42..45 0.033 100.4 37.6 0.4517 0.0082 0.0181 0.8 0.7
45..14 0.198 100.4 37.6 0.4517 0.0496 0.1098 5.0 4.1
45..46 0.061 100.4 37.6 0.4517 0.0153 0.0338 1.5 1.3
46..15 0.000 100.4 37.6 0.4517 0.0000 0.0000 0.0 0.0
46..16 0.000 100.4 37.6 0.4517 0.0000 0.0000 0.0 0.0
40..47 0.032 100.4 37.6 0.4517 0.0080 0.0178 0.8 0.7
47..48 0.204 100.4 37.6 0.4517 0.0510 0.1129 5.1 4.2
48..19 0.225 100.4 37.6 0.4517 0.0563 0.1246 5.7 4.7
48..21 0.126 100.4 37.6 0.4517 0.0315 0.0697 3.2 2.6
47..20 0.298 100.4 37.6 0.4517 0.0746 0.1651 7.5 6.2
tree length for dN: 0.9913
tree length for dS: 2.1945
Gene 2 ls: 88 npatt: 88
Nei & Gojobori 1986. dN/dS (dN, dS)
(Pairwise deletion)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)
__1_H._rufescens
__2_H._sorenseni 3.0851 (0.0797 0.0258)
__3_H._walallensis 4.1572 (0.1252 0.0301) 1.1778 (0.0663 0.0563)
__4_H._kamtschatkana 3.1751 (0.1411 0.0444) 2.1800 (0.1156 0.0530) 2.1578 (0.1638 0.0759)
__5_H._sieboldii 1.4894 (0.1645 0.1105) 1.2695 (0.1600 0.1261) 1.2975 (0.1808 0.1393) 1.2281 (0.1888 0.1538)
__6_H._discus_hannai 2.1926 (0.2539 0.1158) 1.7430 (0.2288 0.1313) 1.4284 (0.2213 0.1549) 1.9418 (0.2671 0.1375) 1.0938 (0.0823 0.0753)
__7_H._gigantea 2.3613 (0.2502 0.1060) 1.8558 (0.2253 0.1214) 1.5040 (0.2178 0.1448) 2.0671 (0.2634 0.1274) 1.2127 (0.0796 0.0656)-1.0000 (0.0098 0.0000)
__8_H._corrugata 1.2782 (0.2116 0.1656) 1.2794 (0.1961 0.1533) 1.2467 (0.2160 0.1733) 1.6515 (0.2498 0.1513) 1.7753 (0.1747 0.0984) 3.1717 (0.2474 0.0780) 3.5463 (0.2437 0.0687)
__9_H._cracherodii 2.2617 (0.3260 0.1441) 2.0769 (0.3099 0.1492) 1.9543 (0.3182 0.1628) 2.0139 (0.3794 0.1884) 4.6321 (0.2105 0.0454) 2.6039 (0.2412 0.0926) 2.9430 (0.2444 0.0830) 1.7528 (0.2017 0.1151)
_10_H._fulgens 1.4424 (0.3459 0.2398) 1.4338 (0.3394 0.2367) 1.1772 (0.3321 0.2821) 1.1489 (0.3004 0.2614) 2.2652 (0.3581 0.1581) 1.9382 (0.3503 0.1808) 1.8453 (0.3344 0.1812) 2.2605 (0.3402 0.1505) 2.8395 (0.4073 0.1434)
_11_H._roei 0.5771 (0.5167 0.8953) 0.5437 (0.4864 0.8947) 0.5316 (0.5060 0.9518) 0.6222 (0.5419 0.8709) 0.5827 (0.4540 0.7792) 0.5347 (0.5164 0.9658) 0.5675 (0.5159 0.9091) 0.4532 (0.4311 0.9513) 0.5700 (0.4932 0.8652) 0.6099 (0.4629 0.7590)
_12_H._scalaris 0.4979 (0.5699 1.1445) 0.4448 (0.5072 1.1403) 0.4147 (0.5149 1.2414) 0.5264 (0.5860 1.1132) 0.4655 (0.4713 1.0124) 0.4274 (0.5372 1.2570) 0.4562 (0.5366 1.1763) 0.3354 (0.4065 1.2118) 0.3765 (0.4761 1.2647) 0.6796 (0.5835 0.8586) 1.8936 (0.1473 0.0778)
_13_H._laevigata 0.5562 (0.5578 1.0030) 0.4954 (0.4959 1.0011) 0.4648 (0.5034 1.0831) 0.5989 (0.5847 0.9762) 0.4091 (0.4356 1.0647) 0.4270 (0.5198 1.2172) 0.4550 (0.5192 1.1413) 0.4036 (0.4441 1.1004) 0.4879 (0.5185 1.0627) 0.6695 (0.5246 0.7835) 1.4746 (0.1317 0.0893) 2.1505 (0.1242 0.0578)
_14_H._cyclobates 0.7877 (0.6659 0.8453) 0.8286 (0.6188 0.7468) 0.6513 (0.6198 0.9516) 0.8774 (0.7213 0.8220) 0.7704 (0.6545 0.8495) 0.7124 (0.7194 1.0097) 0.7701 (0.7314 0.9498) 0.7017 (0.5955 0.8487) 0.8720 (0.6907 0.7921) 0.9663 (0.6498 0.6724) 2.2570 (0.3224 0.1428) 1.6782 (0.3147 0.1875) 1.9910 (0.3047 0.1530)
_15_H._rubra 0.6413 (0.5541 0.8641) 0.6199 (0.5028 0.8110) 0.5357 (0.5005 0.9343) 0.6910 (0.5805 0.8400) 0.5983 (0.4790 0.8005) 0.4884 (0.5150 1.0543) 0.5196 (0.5145 0.9901) 0.4967 (0.4420 0.8900) 0.6601 (0.5421 0.8212) 0.8811 (0.5699 0.6467) 1.7842 (0.1718 0.0963) 1.6062 (0.1958 0.1219) 1.2472 (0.1668 0.1337) 1.4405 (0.2299 0.1596)
_16_H._conicopora 0.6413 (0.5541 0.8641) 0.6199 (0.5028 0.8110) 0.5357 (0.5005 0.9343) 0.6910 (0.5805 0.8400) 0.5983 (0.4790 0.8005) 0.5073 (0.5349 1.0543) 0.5397 (0.5344 0.9901) 0.4967 (0.4420 0.8900) 0.6355 (0.5219 0.8212) 0.8811 (0.5699 0.6467) 1.7842 (0.1718 0.0963) 1.6062 (0.1958 0.1219) 1.2472 (0.1668 0.1337) 1.3952 (0.2176 0.1560)-1.0000 (0.0100 0.0000)
_17_H._pustulata 0.7014 (0.6875 0.9801) 0.6685 (0.5973 0.8935) 0.5567 (0.5975 1.0732) 0.6083 (0.6381 1.0491) 0.5430 (0.5635 1.0377) 0.5776 (0.5789 1.0023) 0.6118 (0.5783 0.9453) 0.4990 (0.4875 0.9770) 0.6325 (0.5906 0.9337) 0.6152 (0.5356 0.8706) 0.4849 (0.2328 0.4801) 0.6146 (0.2548 0.4145) 0.6559 (0.2440 0.3720) 0.8176 (0.3624 0.4433) 0.4249 (0.1882 0.4431) 0.4396 (0.1948 0.4431)
_18_H._midae 0.5126 (0.5375 1.0486) 0.5254 (0.5011 0.9537) 0.4365 (0.4938 1.1313) 0.4441 (0.5531 1.2455) 0.5253 (0.4675 0.8899) 0.4065 (0.4665 1.1476) 0.4220 (0.4708 1.1157) 0.3246 (0.3613 1.1128) 0.4293 (0.3906 0.9099) 0.3632 (0.3525 0.9705) 0.8427 (0.2302 0.2731) 0.8669 (0.2580 0.2976) 0.8313 (0.2658 0.3197) 1.2925 (0.4167 0.3224) 1.0804 (0.3245 0.3003) 1.0804 (0.3245 0.3003) 0.6839 (0.2991 0.4373)
_19_H._ovina 0.7116 (0.5987 0.8413) 0.6778 (0.5265 0.7768) 0.5631 (0.5182 0.9203) 0.6315 (0.5498 0.8706) 0.8008 (0.5822 0.7270) 0.6276 (0.6169 0.9829) 0.6650 (0.6162 0.9267) 0.5642 (0.4885 0.8658) 0.9159 (0.6176 0.6743) 0.7549 (0.5321 0.7049) 1.4721 (0.2262 0.1537) 0.9816 (0.2443 0.2489) 1.0558 (0.2166 0.2051) 1.0833 (0.2835 0.2617) 0.8217 (0.2138 0.2602) 0.8217 (0.2138 0.2602) 0.5443 (0.2449 0.4500) 1.2059 (0.3711 0.3078)
_20_H._diversicolor 0.5882 (0.5444 0.9256) 0.5767 (0.4884 0.8469) 0.4870 (0.4891 1.0043) 0.5522 (0.5290 0.9579) 0.6858 (0.5746 0.8378) 0.6052 (0.5492 0.9074) 0.6641 (0.5697 0.8580) 0.5587 (0.5060 0.9057) 0.7764 (0.6340 0.8165) 0.9057 (0.5708 0.6302) 0.9983 (0.2953 0.2958) 0.7371 (0.2839 0.3852) 0.8224 (0.2977 0.3621) 1.5670 (0.4863 0.3103) 1.2351 (0.3923 0.3176) 1.2895 (0.4096 0.3176) 0.6207 (0.3464 0.5581) 0.5962 (0.3030 0.5083) 1.1307 (0.2472 0.2186)
_21_H._varia 0.6445 (0.5992 0.9298) 0.5722 (0.5261 0.9196) 0.5295 (0.5086 0.9605) 0.5432 (0.5287 0.9733) 0.6820 (0.5669 0.8312) 0.5058 (0.5768 1.1404) 0.5371 (0.5762 1.0728) 0.4602 (0.4490 0.9756) 0.6788 (0.5896 0.8687) 0.6475 (0.5107 0.7887) 0.9265 (0.3015 0.3254) 0.7296 (0.3284 0.4501) 0.8481 (0.3472 0.4093) 0.8095 (0.4598 0.5680) 0.7611 (0.3503 0.4603) 0.7266 (0.3345 0.4603) 0.5718 (0.3168 0.5540) 0.8403 (0.3767 0.4483) 0.8002 (0.1972 0.2464) 0.5669 (0.2537 0.4475)
_22_H._australis 0.7026 (0.5533 0.7875) 0.6123 (0.4826 0.7881) 0.5369 (0.4460 0.8308) 0.6656 (0.5310 0.7978) 0.7626 (0.5035 0.6603) 0.6175 (0.4780 0.7740) 0.6790 (0.4966 0.7313) 0.6926 (0.4759 0.6870) 0.8504 (0.5392 0.6340) 0.8734 (0.4892 0.5602) 0.8961 (0.2390 0.2667) 0.8373 (0.2611 0.3119) 0.7163 (0.2202 0.3074) 1.1301 (0.3985 0.3526) 0.8953 (0.2878 0.3215) 0.9417 (0.3027 0.3215) 0.7207 (0.3093 0.4292) 0.8059 (0.3188 0.3956) 0.6921 (0.2477 0.3579) 0.4466 (0.2033 0.4552) 0.6539 (0.3299 0.5046)
_23_H._t.tuberculata 0.7363 (0.5888 0.7996) 0.8396 (0.6073 0.7233) 0.7659 (0.6229 0.8133) 0.6912 (0.6589 0.9533) 0.7500 (0.5832 0.7776) 0.8114 (0.6422 0.7916) 0.8266 (0.6350 0.7683) 0.6818 (0.5419 0.7948) 0.7483 (0.5637 0.7533) 0.7067 (0.5919 0.8375) 1.1997 (0.3321 0.2769) 1.1470 (0.3567 0.3110) 1.3978 (0.3648 0.2610) 1.4357 (0.4044 0.2816) 0.9638 (0.2904 0.3013) 0.9176 (0.2808 0.3060) 1.3640 (0.2673 0.1959) 1.6078 (0.4075 0.2534) 1.3334 (0.3987 0.2990) 1.1483 (0.5220 0.4545) 0.8905 (0.4993 0.5607) 1.3561 (0.4164 0.3071)
_24_H._t.coccinea 0.7331 (0.5702 0.7778) 0.8747 (0.5943 0.6795) 0.6679 (0.5850 0.8759) 0.8262 (0.6449 0.7805) 0.7821 (0.5708 0.7298) 0.9067 (0.6286 0.6933) 0.9244 (0.6216 0.6724) 0.8474 (0.5358 0.6323) 0.7380 (0.5623 0.7618) 0.7057 (0.6016 0.8524) 1.1325 (0.3486 0.3078) 1.1132 (0.3829 0.3440) 1.2812 (0.3726 0.2908) 1.1755 (0.4028 0.3427) 0.9398 (0.3144 0.3345) 0.8968 (0.3045 0.3396) 1.5392 (0.2869 0.1864) 1.7011 (0.4359 0.2562) 1.5290 (0.4416 0.2888) 1.2883 (0.5721 0.4441) 0.9967 (0.5477 0.5495) 1.0932 (0.4345 0.3975) 1.0664 (0.0401 0.0376)
_25_H._iris 0.9368 (0.7050 0.7526) 0.8462 (0.6504 0.7686) 0.9454 (0.6772 0.7163) 0.7951 (0.6506 0.8183) 1.0182 (0.6605 0.6487) 1.0235 (0.7299 0.7131) 1.0599 (0.7357 0.6942) 0.8721 (0.6100 0.6995) 1.0467 (0.7034 0.6721) 0.7729 (0.6093 0.7884) 0.8242 (0.4345 0.5272) 0.6968 (0.4502 0.6461) 0.7848 (0.4636 0.5907) 0.8465 (0.4869 0.5752) 0.9575 (0.4722 0.4932) 0.9192 (0.4534 0.4932) 0.6208 (0.4775 0.7693) 0.4336 (0.4079 0.9408) 0.4861 (0.3351 0.6895) 0.4013 (0.3373 0.8405) 0.5013 (0.4307 0.8590) 0.6982 (0.4419 0.6328) 1.1239 (0.5726 0.5095) 1.0965 (0.6068 0.5534)
TREE # 1: ((10, (((4, (1, (2, 3))), (5, (6, 7))), (8, 9))), 25, ((17, (24, 23)), (22, ((18, ((11, (12, 13)), (14, (15, 16)))), ((19, 21), 20))))); MP score: -1
lnL(ntime: 47 np: 49): -3517.005213 +0.000000
26..27 27..10 27..28 28..29 29..30 30..4 30..31 31..1 31..32 32..2 32..3 29..33 33..5 33..34 34..6 34..7 28..35 35..8 35..9 26..25 26..36 36..37 37..17 37..38 38..24 38..23 36..39 39..22 39..40 40..41 41..18 41..42 42..43 43..11 43..44 44..12 44..13 42..45 45..14 45..46 46..15 46..16 40..47 47..48 48..19 48..21 47..20
0.757565 0.476861 0.246877 0.101331 0.211848 0.227653 0.038465 0.133924 0.036179 0.033302 0.160850 0.129865 0.034379 0.193652 0.022727 0.000004 0.053108 0.172041 0.409665 0.912956 0.157156 0.336114 0.302303 0.433865 0.102707 0.013558 0.072923 0.407694 0.040965 0.119416 0.619635 0.086549 0.034108 0.147170 0.119393 0.202723 0.126699 0.222615 0.516318 0.130302 0.023269 0.000004 0.181234 0.135725 0.179824 0.476106 0.442244 1.504858 1.267585
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 9.98387
((10: 0.476861, (((4: 0.227653, (1: 0.133924, (2: 0.033302, 3: 0.160850): 0.036179): 0.038465): 0.211848, (5: 0.034379, (6: 0.022727, 7: 0.000004): 0.193652): 0.129865): 0.101331, (8: 0.172041, 9: 0.409665): 0.053108): 0.246877): 0.757565, 25: 0.912956, ((17: 0.302303, (24: 0.102707, 23: 0.013558): 0.433865): 0.336114, (22: 0.407694, ((18: 0.619635, ((11: 0.147170, (12: 0.202723, 13: 0.126699): 0.119393): 0.034108, (14: 0.516318, (15: 0.023269, 16: 0.000004): 0.130302): 0.222615): 0.086549): 0.119416, ((19: 0.179824, 21: 0.476106): 0.135725, 20: 0.442244): 0.181234): 0.040965): 0.072923): 0.157156);
((_10_H._fulgens: 0.476861, (((__4_H._kamtschatkana: 0.227653, (__1_H._rufescens: 0.133924, (__2_H._sorenseni: 0.033302, __3_H._walallensis: 0.160850): 0.036179): 0.038465): 0.211848, (__5_H._sieboldii: 0.034379, (__6_H._discus_hannai: 0.022727, __7_H._gigantea: 0.000004): 0.193652): 0.129865): 0.101331, (__8_H._corrugata: 0.172041, __9_H._cracherodii: 0.409665): 0.053108): 0.246877): 0.757565, _25_H._iris: 0.912956, ((_17_H._pustulata: 0.302303, (_24_H._t.coccinea: 0.102707, _23_H._t.tuberculata: 0.013558): 0.433865): 0.336114, (_22_H._australis: 0.407694, ((_18_H._midae: 0.619635, ((_11_H._roei: 0.147170, (_12_H._scalaris: 0.202723, _13_H._laevigata: 0.126699): 0.119393): 0.034108, (_14_H._cyclobates: 0.516318, (_15_H._rubra: 0.023269, _16_H._conicopora: 0.000004): 0.130302): 0.222615): 0.086549): 0.119416, ((_19_H._ovina: 0.179824, _21_H._varia: 0.476106): 0.135725, _20_H._diversicolor: 0.442244): 0.181234): 0.040965): 0.072923): 0.157156);
Detailed output identifying parameters
kappa (ts/tv) = 1.50486
omega (dN/dS) = 1.26758
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
26..27 0.758 200.7 63.3 1.2676 0.2660 0.2098 53.4 13.3
27..10 0.477 200.7 63.3 1.2676 0.1674 0.1321 33.6 8.4
27..28 0.247 200.7 63.3 1.2676 0.0867 0.0684 17.4 4.3
28..29 0.101 200.7 63.3 1.2676 0.0356 0.0281 7.1 1.8
29..30 0.212 200.7 63.3 1.2676 0.0744 0.0587 14.9 3.7
30..4 0.228 200.7 63.3 1.2676 0.0799 0.0631 16.0 4.0
30..31 0.038 200.7 63.3 1.2676 0.0135 0.0107 2.7 0.7
31..1 0.134 200.7 63.3 1.2676 0.0470 0.0371 9.4 2.3
31..32 0.036 200.7 63.3 1.2676 0.0127 0.0100 2.5 0.6
32..2 0.033 200.7 63.3 1.2676 0.0117 0.0092 2.3 0.6
32..3 0.161 200.7 63.3 1.2676 0.0565 0.0446 11.3 2.8
29..33 0.130 200.7 63.3 1.2676 0.0456 0.0360 9.2 2.3
33..5 0.034 200.7 63.3 1.2676 0.0121 0.0095 2.4 0.6
33..34 0.194 200.7 63.3 1.2676 0.0680 0.0536 13.6 3.4
34..6 0.023 200.7 63.3 1.2676 0.0080 0.0063 1.6 0.4
34..7 0.000 200.7 63.3 1.2676 0.0000 0.0000 0.0 0.0
28..35 0.053 200.7 63.3 1.2676 0.0186 0.0147 3.7 0.9
35..8 0.172 200.7 63.3 1.2676 0.0604 0.0477 12.1 3.0
35..9 0.410 200.7 63.3 1.2676 0.1438 0.1135 28.9 7.2
26..25 0.913 200.7 63.3 1.2676 0.3206 0.2529 64.3 16.0
26..36 0.157 200.7 63.3 1.2676 0.0552 0.0435 11.1 2.8
36..37 0.336 200.7 63.3 1.2676 0.1180 0.0931 23.7 5.9
37..17 0.302 200.7 63.3 1.2676 0.1061 0.0837 21.3 5.3
37..38 0.434 200.7 63.3 1.2676 0.1523 0.1202 30.6 7.6
38..24 0.103 200.7 63.3 1.2676 0.0361 0.0284 7.2 1.8
38..23 0.014 200.7 63.3 1.2676 0.0048 0.0038 1.0 0.2
36..39 0.073 200.7 63.3 1.2676 0.0256 0.0202 5.1 1.3
39..22 0.408 200.7 63.3 1.2676 0.1431 0.1129 28.7 7.2
39..40 0.041 200.7 63.3 1.2676 0.0144 0.0113 2.9 0.7
40..41 0.119 200.7 63.3 1.2676 0.0419 0.0331 8.4 2.1
41..18 0.620 200.7 63.3 1.2676 0.2176 0.1716 43.7 10.9
41..42 0.087 200.7 63.3 1.2676 0.0304 0.0240 6.1 1.5
42..43 0.034 200.7 63.3 1.2676 0.0120 0.0094 2.4 0.6
43..11 0.147 200.7 63.3 1.2676 0.0517 0.0408 10.4 2.6
43..44 0.119 200.7 63.3 1.2676 0.0419 0.0331 8.4 2.1
44..12 0.203 200.7 63.3 1.2676 0.0712 0.0562 14.3 3.6
44..13 0.127 200.7 63.3 1.2676 0.0445 0.0351 8.9 2.2
42..45 0.223 200.7 63.3 1.2676 0.0782 0.0617 15.7 3.9
45..14 0.516 200.7 63.3 1.2676 0.1813 0.1430 36.4 9.1
45..46 0.130 200.7 63.3 1.2676 0.0458 0.0361 9.2 2.3
46..15 0.023 200.7 63.3 1.2676 0.0082 0.0064 1.6 0.4
46..16 0.000 200.7 63.3 1.2676 0.0000 0.0000 0.0 0.0
40..47 0.181 200.7 63.3 1.2676 0.0636 0.0502 12.8 3.2
47..48 0.136 200.7 63.3 1.2676 0.0477 0.0376 9.6 2.4
48..19 0.180 200.7 63.3 1.2676 0.0631 0.0498 12.7 3.2
48..21 0.476 200.7 63.3 1.2676 0.1672 0.1319 33.5 8.4
47..20 0.442 200.7 63.3 1.2676 0.1553 0.1225 31.2 7.8
tree length for dN: 3.5055
tree length for dS: 2.7655
Time used: 6:00
|
