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小小的散

新虫 (初入文坛)

应助: 0 (幼儿园)
金币: 52.4
帖子: 13
在线: 3.2小时
虫号: 3030264
注册: 2014-03-08
专业: 生物信息学

[求助] 用pamlx做codeml的结果怎么分析？已有1人参与

小虫想用codeml观察某个基因在进化过程中是正选择还是负选择，请问应该怎么分析下面的结果呢？
不胜感激

pamlx的输出结果：
15       verbose | verbose             1.00
  7       runmode | runmode             0.00
  4       seqtype | seqtype             1.00
13    CodonFreq | CodonFreq             0.00
14       estFreq | estFreq             0.00
34          ndata | ndata                1.00
  9          clock | clock                0.00
18       aaDist | aaDist                0.00
16          model | model                0.00
20       NSsites | NSsites             0.00
22          icode | icode                0.00
23          Mgene | Mgene                0.00
24    fix_kappa | fix_kappa             0.00
25          kappa | kappa                2.00
26    fix_omega | fix_omega             0.00
27          omega | omega                0.40
28    fix_alpha | fix_alpha             1.00
29          alpha | alpha                0.00
30       Malpha | Malpha                0.00
31          ncatG | ncatG                5.00
11          getSE | getSE                1.00
12 RateAncestor | RateAncestor          0.00
36    Small_Diff | Small_Diff          0.00
  6    cleandata | cleandata             0.00
37    fix_blength | fix_blength          0.00
  8       method | method                0.00
CODONML in paml version 4.7, January 2013

----------------------------------------------
Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT
   TTC |    TCC |    TAC |    TGC
Leu L TTA |    TCA | *** * TAA | *** * TGA
   TTG |    TCG |    TAG | Trp W TGG
----------------------------------------------
Leu L CTT | Pro P CCT | His H CAT | Arg R CGT
   CTC |    CCC |    CAC |    CGC
   CTA |    CCA | Gln Q CAA |    CGA
   CTG |    CCG |    CAG |    CGG
----------------------------------------------
Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT
   ATC |    ACC |    AAC |    AGC
   ATA |    ACA | Lys K AAA | Arg R AGA
Met M ATG |    ACG |    AAG |    AGG
----------------------------------------------
Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT
   GTC |    GCC |    GAC |    GGC
   GTA |    GCA | Glu E GAA |    GGA
   GTG |    GCG |    GAG |    GGG
----------------------------------------------
Nice code, uuh?

Ambiguity character definition table:

T (1): T
C (1): C
A (1): A
G (1): G
U (1): T
Y (2): T C
R (2): A G
M (2): C A
K (2): T G
S (2): C G
W (2): T A
H (3): T C A
B (3): T C G
V (3): C A G
D (3): T A G
- (4): T C A G
N (4): T C A G
? (4): T C A G

ns = 13    ls = 273
Reading sequences, sequential format..
Reading seq # 1: U68496
Reading seq # 2: U68497
Reading seq # 3: U68498
Reading seq # 4: U68499
Reading seq # 5: U68500
Reading seq # 6: U68501
Reading seq # 7: U68502
Reading seq # 8: U68503
Reading seq # 9: U68504
Reading seq #10: U68505
Reading seq #11: U68506
Reading seq #12: U68507
Reading seq #13: U68508

Sequences read..
Counting site patterns..  0:00

      79 patterns at    91 /    91 sites (100.0%),  0:00
Counting codons..
NG distances for seqs.:
1
  2 1:Sites 59.8 +  213.2 =  273.0 Diffs    3.0 + 6.0 = 9.0 2
  3 1:Sites 60.4 +  212.6 =  273.0 Diffs    1.5 + 18.5 = 20.0
  3 2:Sites 60.3 +  212.7 =  273.0 Diffs    1.5 + 22.5 = 24.0 3
  4 1:Sites 59.5 +  213.5 =  273.0 Diffs    1.5 + 19.5 = 21.0
  4 2:Sites 59.4 +  213.6 =  273.0 Diffs    1.5 + 21.5 = 23.0
  4 3:Sites 59.9 +  213.1 =  273.0 Diffs    0.0 + 14.0 = 14.0 4
  5 1:Sites 59.0 +  214.0 =  273.0 Diffs    2.5 + 25.5 = 28.0
  5 2:Sites 58.9 +  214.1 =  273.0 Diffs    2.5 + 27.5 = 30.0
  5 3:Sites 59.5 +  213.5 =  273.0 Diffs    2.5 + 16.5 = 19.0
  5 4:Sites 58.6 +  214.4 =  273.0 Diffs    1.0 + 10.0 = 11.0 5
  6 1:Sites 60.1 +  212.9 =  273.0 Diffs    2.5 + 23.5 = 26.0
  6 2:Sites 60.0 +  213.0 =  273.0 Diffs    2.5 + 27.5 = 30.0
  6 3:Sites 60.5 +  212.5 =  273.0 Diffs    1.0 + 19.0 = 20.0
  6 4:Sites 59.6 +  213.4 =  273.0 Diffs    1.0 + 25.0 = 26.0
  6 5:Sites 59.2 +  213.8 =  273.0 Diffs    3.5 + 27.5 = 31.0 6
  7 1:Sites 60.3 +  212.7 =  273.0 Diffs    5.8 + 31.2 = 37.0
  7 2:Sites 60.2 +  212.8 =  273.0 Diffs    5.3 + 33.7 = 39.0
  7 3:Sites 60.8 +  212.2 =  273.0 Diffs    3.8 + 24.2 = 28.0
  7 4:Sites 59.9 +  213.1 =  273.0 Diffs    3.8 + 25.2 = 29.0
  7 5:Sites 59.4 +  213.6 =  273.0 Diffs    6.3 + 29.7 = 36.0
  7 6:Sites 60.5 +  212.5 =  273.0 Diffs    2.3 + 26.7 = 29.0 7
  8 1:Sites 60.1 +  212.9 =  273.0 Diffs    3.5 + 28.5 = 32.0
  8 2:Sites 60.0 +  213.0 =  273.0 Diffs    3.5 + 28.5 = 32.0
  8 3:Sites 60.6 +  212.5 =  273.0 Diffs    2.5 + 24.5 = 27.0
  8 4:Sites 59.7 +  213.3 =  273.0 Diffs    2.5 + 26.5 = 29.0
  8 5:Sites 59.2 +  213.8 =  273.0 Diffs    4.0 + 28.0 = 32.0
  8 6:Sites 60.3 +  212.7 =  273.0 Diffs    3.5 + 27.5 = 31.0
  8 7:Sites 60.5 +  212.5 =  273.0 Diffs    7.5 + 25.5 = 33.0 8
  9 1:Sites 59.9 +  213.2 =  273.0 Diffs    4.0 + 26.0 = 30.0
  9 2:Sites 59.7 +  213.3 =  273.0 Diffs    6.0 + 28.0 = 34.0
  9 3:Sites 60.3 +  212.7 =  273.0 Diffs    5.0 + 20.0 = 25.0
  9 4:Sites 59.4 +  213.6 =  273.0 Diffs    4.5 + 20.5 = 25.0
  9 5:Sites 58.9 +  214.1 =  273.0 Diffs    6.5 + 24.5 = 31.0
  9 6:Sites 60.0 +  213.0 =  273.0 Diffs    6.5 + 20.5 = 27.0
  9 7:Sites 60.3 +  212.7 =  273.0 Diffs    7.8 + 21.2 = 29.0
  9 8:Sites 60.0 +  213.0 =  273.0 Diffs    7.0 + 23.0 = 30.0 9
10 1:Sites 59.7 +  213.3 =  273.0 Diffs    5.0 + 25.0 = 30.0
10 2:Sites 59.6 +  213.4 =  273.0 Diffs    5.0 + 27.0 = 32.0
10 3:Sites 60.1 +  212.9 =  273.0 Diffs    4.0 + 19.0 = 23.0
10 4:Sites 59.2 +  213.8 =  273.0 Diffs    3.5 + 20.5 = 24.0
10 5:Sites 58.8 +  214.2 =  273.0 Diffs    5.5 + 24.5 = 30.0
10 6:Sites 59.8 +  213.2 =  273.0 Diffs    4.5 + 22.5 = 27.0
10 7:Sites 60.1 +  212.9 =  273.0 Diffs    6.8 + 20.2 = 27.0
10 8:Sites 59.9 +  213.2 =  273.0 Diffs    4.0 + 24.0 = 28.0
10 9:Sites 59.6 +  213.4 =  273.0 Diffs    4.0 + 4.0 = 8.0  10
11 1:Sites 59.9 +  213.1 =  273.0 Diffs    2.5 + 26.5 = 29.0
11 2:Sites 59.8 +  213.2 =  273.0 Diffs    5.5 + 28.5 = 34.0
11 3:Sites 60.4 +  212.6 =  273.0 Diffs    4.5 + 23.5 = 28.0
11 4:Sites 59.5 +  213.5 =  273.0 Diffs    4.0 + 24.0 = 28.0
11 5:Sites 59.0 +  214.0 =  273.0 Diffs    5.5 + 27.5 = 33.0
11 6:Sites 60.1 +  212.9 =  273.0 Diffs    6.0 + 22.0 = 28.0
11 7:Sites 60.4 +  212.6 =  273.0 Diffs    8.3 + 24.7 = 33.0
11 8:Sites 60.1 +  212.9 =  273.0 Diffs    6.5 + 26.5 = 33.0
11 9:Sites 59.9 +  213.1 =  273.0 Diffs    3.5 + 4.5 = 8.0
11  10:Sites 59.7 +  213.3 =  273.0 Diffs    5.5 + 8.5 = 14.0  11
12 1:Sites 60.5 +  212.5 =  273.0 Diffs    4.5 + 29.5 = 34.0
12 2:Sites 60.4 +  212.6 =  273.0 Diffs    4.5 + 33.5 = 38.0
12 3:Sites 61.0 +  212.0 =  273.0 Diffs    3.5 + 19.5 = 23.0
12 4:Sites 60.1 +  212.9 =  273.0 Diffs    3.5 + 22.5 = 26.0
12 5:Sites 59.6 +  213.4 =  273.0 Diffs    5.0 + 26.0 = 31.0
12 6:Sites 60.7 +  212.3 =  273.0 Diffs    4.5 + 24.5 = 29.0
12 7:Sites 60.9 +  212.1 =  273.0 Diffs    7.3 + 21.7 = 29.0
12 8:Sites 60.7 +  212.3 =  273.0 Diffs    4.0 + 24.0 = 28.0
12 9:Sites 60.4 +  212.6 =  273.0 Diffs    6.0 + 9.0 = 15.0
12  10:Sites 60.3 +  212.7 =  273.0 Diffs    2.0 + 9.0 = 11.0
12  11:Sites 60.5 +  212.5 =  273.0 Diffs    5.5 + 9.5 = 15.0  12
13 1:Sites 59.9 +  213.1 =  273.0 Diffs    4.5 + 36.5 = 41.0
13 2:Sites 59.8 +  213.2 =  273.0 Diffs    4.5 + 36.5 = 41.0

13 3:Sites 60.4 +  212.6 =  273.0 Diffs    4.0 + 30.0 = 34.0
13 4:Sites 59.5 +  213.5 =  273.0 Diffs    4.0 + 27.0 = 31.0
13 5:Sites 59.0 +  214.0 =  273.0 Diffs    5.0 + 26.0 = 31.0
13 6:Sites 60.1 +  212.9 =  273.0 Diffs    6.0 + 28.0 = 34.0
13 7:Sites 60.4 +  212.6 =  273.0 Diffs    8.3 + 26.7 = 35.0
13 8:Sites 60.1 +  212.9 =  273.0 Diffs    5.0 + 27.0 = 32.0
13 9:Sites 59.9 +  213.1 =  273.0 Diffs    6.5 + 21.5 = 28.0
13  10:Sites 59.7 +  213.3 =  273.0 Diffs    2.5 + 22.5 = 25.0
13  11:Sites 60.0 +  213.0 =  273.0 Diffs    6.0 + 25.0 = 31.0
13  12:Sites 60.5 +  212.5 =  273.0 Diffs    2.5 + 22.5 = 25.0  13

   624 bytes for distance
77104 bytes for conP
      0 bytes for fhK
  5000000 bytes for space

TREE #  1
(1, 2, ((3, (4, 5)), (6, (7, (8, ((((9, 11), 10), 12), 13)))))); MP score: 136
1 0.231603
2 0.118697
3 0.105762
4 0.103763
5 0.103653
6 0.103627
7 0.103622
8 0.103621
9 0.103621
  10 0.103621
424072 bytes for conP, adjusted

0.033457 0.069836 0.113609 0.025446 0.076423 0.051361 0.027202 0.080448 0.042832 0.130329 0.033338 0.171651 0.000000 0.149217 0.040489 0.059854 0.009691 0.044490 0.031077 0.049686 0.039922 0.083111 0.177533 2.000000 0.400000

ntime & nrate & np: 23    2 25

Bounds (np=25):
0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000100
  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000 999.000000 999.000000

np = 25
lnL0 = -1220.231096

Iterating by ming2
Initial: fx=  1220.231096
x=  0.03346  0.06984  0.11361  0.02545  0.07642  0.05136  0.02720  0.08045  0.04283  0.13033  0.03334  0.17165  0.00000  0.14922  0.04049  0.05985  0.00969  0.04449  0.03108  0.04969  0.03992  0.08311  0.17753  2.00000  0.40000

  1 h-m-p  0.0000 0.0007 469.0061 ++YYCCCC  1211.002298  5 0.0003 40 | 0/25
  2 h-m-p  0.0002 0.0008 132.5623 +CYYC  1203.765909  3 0.0007 73 | 0/25
  3 h-m-p  0.0001 0.0004 418.8964 YCYC 1200.900766  3 0.0002 105 | 0/25
  4 h-m-p  0.0004 0.0018 195.2846 YCCC 1196.208152  3 0.0008 138 | 0/25
  5 h-m-p  0.0001 0.0007 155.9189 +YYYYC  1192.968013  4 0.0005 171 | 0/25
  6 h-m-p  0.0001 0.0007 225.3270 YCCCC  1190.879786  4 0.0004 206 | 0/25
  7 h-m-p  0.0004 0.0019 133.2646 CCC 1189.925119  2 0.0004 238 | 0/25
  8 h-m-p  0.0007 0.0034  52.9874 CYC 1189.435621  2 0.0006 269 | 0/25
  9 h-m-p  0.0011 0.0054  28.7714 YYC 1189.173515  2 0.0010 299 | 0/25
10 h-m-p  0.0016 0.0154  17.3933 YC    1189.092352  1 0.0008 328 | 0/25
11 h-m-p  0.0022 0.0407 6.7537 CCC 1189.058260  2 0.0017 360 | 0/25
12 h-m-p  0.0014 0.0496 8.4704 YC    1188.992811  1 0.0031 389 | 0/25
13 h-m-p  0.0013 0.0452  20.2523 +YC 1188.822413  1 0.0037 419 | 0/25
14 h-m-p  0.0014 0.0203  54.5600 +YYYC  1188.196056  3 0.0052 451 | 0/25
15 h-m-p  0.0016 0.0080 149.1999 YCCC 1187.814327  3 0.0012 484 | 0/25
16 h-m-p  0.0017 0.0085  37.8110 YCC 1187.736402  2 0.0009 515 | 0/25
17 h-m-p  0.0024 0.0321  14.7235 YCC 1187.679796  2 0.0018 546 | 0/25
18 h-m-p  0.0041 0.0203 2.6057 YC    1187.666994  1 0.0020 575 | 0/25
19 h-m-p  0.0049 0.1463 1.0970 +CCC 1187.483706  2 0.0211 608 | 0/25
20 h-m-p  0.0019 0.0206  12.3306 +YCCCCC  1186.037745  5 0.0084 646 | 0/25
21 h-m-p  0.0008 0.0039  53.9582 +YCYCCC  1183.940036  5 0.0022 683 | 0/25
22 h-m-p  0.0003 0.0017  48.2643 YCCCC  1183.446020  4 0.0007 718 | 0/25
23 h-m-p  0.0004 0.0019  58.9156 CCCC 1183.089660  3 0.0006 752 | 0/25

24 h-m-p  0.0185 0.1105 1.7835 CY    1183.073174  1 0.0046 782 | 0/25
25 h-m-p  0.0084 0.1357 0.9676 CCC 1183.007084  2 0.0131 814 | 0/25
26 h-m-p  0.0021 0.1075 6.0391 ++YCCC  1181.405622  3 0.0281 874 | 0/25
27 h-m-p  0.0024 0.0121 9.3216 CYC 1181.379436  2 0.0007 905 | 0/25
28 h-m-p  0.0373 2.9850 0.1768 ++YCCC  1180.464300  3 1.2089 940 | 0/25
29 h-m-p  1.6000 8.0000 0.0575 CCC 1180.029465  2 2.5333 997 | 0/25
30 h-m-p  1.6000 8.0000 0.0851 CCC 1179.711214  2 2.4203  1054 | 0/25
31 h-m-p  1.6000 8.0000 0.0605 CCC 1179.643267  2 1.3058  1111 | 0/25
32 h-m-p  1.6000 8.0000 0.0295 CC    1179.629940  1 1.3740  1166 | 0/25
33 h-m-p  1.6000 8.0000 0.0053 C    1179.627401  0 1.5280  1219 | 0/25
34 h-m-p  1.6000 8.0000 0.0023 YC    1179.627116  1 1.1520  1273 | 0/25
35 h-m-p  1.6000 8.0000 0.0010 Y    1179.627100  0 1.1524  1326 | 0/25
36 h-m-p  1.6000 8.0000 0.0000 C    1179.627099  0 1.5731  1379 | 0/25
37 h-m-p  1.1276 8.0000 0.0001 C    1179.627099  0 1.3352  1432 | 0/25
38 h-m-p  1.6000 8.0000 0.0000 Y    1179.627099  0 1.2649  1485 | 0/25
39 h-m-p  1.2958 8.0000 0.0000 C    1179.627099  0 1.3752  1538 | 0/25
40 h-m-p  1.6000 8.0000 0.0000 ----------------..  | 0/25
41 h-m-p  0.0160 8.0000 0.0004 ----Y  1179.627099  0 0.0000  1662
Out..
lnL  = -1179.627099
1663 lfun, 1663 eigenQcodon, 38249 P(t)
Calculating SE's

d123

=  0.00977  0.01025  0.00605  average  0.00869
[B] =  0.00493  0.00503  0.00503  average  0.00499
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.01018 dS =  0.00499 d4 =  0.00519 (47.7 four-fold sites)
         dN*=  0.00973 dS*=  0.00564 S* =  69.55 N* = 203.45

d123

=  0.02803  0.02938  0.01735  average  0.02492
[B] =  0.01414  0.01441  0.01441  average  0.01432
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.02919 dS =  0.01432 d4 =  0.01487 (47.7 four-fold sites)
         dN*=  0.02791 dS*=  0.01616 S* =  69.55 N* = 203.45

d123

=  0.05387  0.05647  0.03334  average  0.04789
[B] =  0.02717  0.02770  0.02770  average  0.02752
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.05611 dS =  0.02752 d4 =  0.02858 (47.7 four-fold sites)
         dN*=  0.05365 dS*=  0.03106 S* =  69.55 N* = 203.45

d123

=  0.00735  0.00770  0.00455  average  0.00653
[B] =  0.00371  0.00378  0.00378  average  0.00375
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.00765 dS =  0.00375 d4 =  0.00390 (47.7 four-fold sites)
         dN*=  0.00732 dS*=  0.00424 S* =  69.55 N* = 203.45

d123

=  0.02318  0.02430  0.01434  average  0.02061
[B] =  0.01169  0.01192  0.01192  average  0.01184
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.02414 dS =  0.01184 d4 =  0.01230 (47.7 four-fold sites)
         dN*=  0.02308 dS*=  0.01336 S* =  69.55 N* = 203.45

d123

=  0.02622  0.02749  0.01623  average  0.02331
[B] =  0.01322  0.01348  0.01348  average  0.01340
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.02731 dS =  0.01340 d4 =  0.01391 (47.7 four-fold sites)
         dN*=  0.02611 dS*=  0.01512 S* =  69.55 N* = 203.45

d123

=  0.00975  0.01022  0.00603  average  0.00867
[B] =  0.00492  0.00501  0.00501  average  0.00498
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.01016 dS =  0.00498 d4 =  0.00517 (47.7 four-fold sites)
         dN*=  0.00971 dS*=  0.00562 S* =  69.55 N* = 203.45

d123

=  0.03741  0.03921  0.02315  average  0.03326
[B] =  0.01887  0.01924  0.01924  average  0.01911
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.03896 dS =  0.01911 d4 =  0.01984 (47.7 four-fold sites)
         dN*=  0.03725 dS*=  0.02157 S* =  69.55 N* = 203.45

d123

=  0.01487  0.01559  0.00920  average  0.01322
[B] =  0.00750  0.00765  0.00765  average  0.00760
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.01549 dS =  0.00760 d4 =  0.00789 (47.7 four-fold sites)
         dN*=  0.01481 dS*=  0.00857 S* =  69.55 N* = 203.45

d123

=  0.05399  0.05660  0.03341  average  0.04800
[B] =  0.02723  0.02776  0.02776  average  0.02759
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.05624 dS =  0.02759 d4 =  0.02864 (47.7 four-fold sites)
         dN*=  0.05377 dS*=  0.03113 S* =  69.55 N* = 203.45

d123

=  0.00978  0.01026  0.00605  average  0.00870
[B] =  0.00493  0.00503  0.00503  average  0.00500
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.01019 dS =  0.00500 d4 =  0.00519 (47.7 four-fold sites)
         dN*=  0.00974 dS*=  0.00564 S* =  69.55 N* = 203.45

d123

=  0.07700  0.08071  0.04765  average  0.06845
[B] =  0.03884  0.03959  0.03959  average  0.03934
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.08020 dS =  0.03934 d4 =  0.04084 (47.7 four-fold sites)
         dN*=  0.07668 dS*=  0.04439 S* =  69.55 N* = 203.45

d123

=  0.01615  0.01693  0.01000  average  0.01436
[B] =  0.00815  0.00831  0.00831  average  0.00825
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.01683 dS =  0.00825 d4 =  0.00857 (47.7 four-fold sites)
         dN*=  0.01609 dS*=  0.00931 S* =  69.55 N* = 203.45

d123

=  0.06712  0.07036  0.04154  average  0.05967
[B] =  0.03385  0.03451  0.03451  average  0.03429
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.06991 dS =  0.03429 d4 =  0.03560 (47.7 four-fold sites)
         dN*=  0.06684 dS*=  0.03870 S* =  69.55 N* = 203.45

d123

=  0.02084  0.02185  0.01290  average  0.01853
[B] =  0.01051  0.01072  0.01072  average  0.01065
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.02171 dS =  0.01065 d4 =  0.01106 (47.7 four-fold sites)
         dN*=  0.02076 dS*=  0.01202 S* =  69.55 N* = 203.45

d123

=  0.01452  0.01522  0.00899  average  0.01291
[B] =  0.00733  0.00747  0.00747  average  0.00742
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.01513 dS =  0.00742 d4 =  0.00770 (47.7 four-fold sites)
         dN*=  0.01446 dS*=  0.00837 S* =  69.55 N* = 203.45

d123

=  0.01542  0.01616  0.00954  average  0.01371
[B] =  0.00778  0.00793  0.00793  average  0.00788
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.01606 dS =  0.00788 d4 =  0.00818 (47.7 four-fold sites)
         dN*=  0.01535 dS*=  0.00889 S* =  69.55 N* = 203.45

d123

=  0.02069  0.02168  0.01280  average  0.01839
[B] =  0.01043  0.01064  0.01064  average  0.01057
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.02155 dS =  0.01057 d4 =  0.01097 (47.7 four-fold sites)
         dN*=  0.02060 dS*=  0.01193 S* =  69.55 N* = 203.45

d123

=  0.00453  0.00474  0.00280  average  0.00402
[B] =  0.00228  0.00233  0.00233  average  0.00231
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.00471 dS =  0.00231 d4 =  0.00240 (47.7 four-fold sites)
         dN*=  0.00451 dS*=  0.00261 S* =  69.55 N* = 203.45

d123

=  0.02864  0.03003  0.01773  average  0.02547
[B] =  0.01445  0.01473  0.01473  average  0.01464
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.02984 dS =  0.01464 d4 =  0.01520 (47.7 four-fold sites)
         dN*=  0.02853 dS*=  0.01652 S* =  69.55 N* = 203.45

d123

=  0.00862  0.00904  0.00534  average  0.00767
[B] =  0.00435  0.00443  0.00443  average  0.00441
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.00898 dS =  0.00441 d4 =  0.00457 (47.7 four-fold sites)
         dN*=  0.00859 dS*=  0.00497 S* =  69.55 N* = 203.45

d123

=  0.02354  0.02467  0.01457  average  0.02093
[B] =  0.01187  0.01210  0.01210  average  0.01203
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.02452 dS =  0.01203 d4 =  0.01249 (47.7 four-fold sites)
         dN*=  0.02344 dS*=  0.01357 S* =  69.55 N* = 203.45

d123

=  0.06998  0.07336  0.04331  average  0.06221
[B] =  0.03530  0.03598  0.03598  average  0.03575
accept  =  1.98259  2.03861  1.20354

w =  2.03861 dN =  0.07289 dS =  0.03575 d4 =  0.03712 (47.7 four-fold sites)
         dN*=  0.06969 dS*=  0.04035 S* =  69.55 N* = 203.45

Time used:  0:26

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1楼 2015-01-10 11:35:35

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

wizardfan

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【答案】应助回帖

感谢参与，应助指数 +1

you really need to read the manual.
The most important concepts: dN, dS, dN/dS and parameters NSsite.

Your selection is to test the whole sequence, not individual sites.