版块导航: 正在加载中...

登录注册

应《网络安全法》要求，自2017年10月1日起，未进行实名认证将不得使用互联网跟帖服务。为保障您的帐号能够正常使用，请尽快对帐号进行手机号验证，感谢您的理解与支持！

24小时热门版块排行榜

北京石油化工学院2026年研究生招生接收调剂公告

返回列表

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

回复此楼

» 猜你喜欢

085600 286分材料求调剂已经有3人回复
275求调剂已经有10人回复
286求调剂已经有6人回复
083000学硕274求调剂已经有5人回复
【求调剂】085601材料工程专硕 | 总分272 | 已经有5人回复
275求调剂已经有13人回复
0856，材料与化工321分求调剂已经有8人回复
085701环境工程，267求调剂已经有12人回复
320分，材料与化工专业，求调剂已经有7人回复
085701环境工程求调剂已经有8人回复

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

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

我用的是example文件...各项设置都是默认的...

搜狗截图20150110113658.png

赞一下

回复此楼

2楼2015-01-10 11:37:56

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

wizardfan

至尊木虫 (著名写手)

BioEPI: 18
应助: 599 (博士)
贵宾: 1.818
金币: 24632.2
散金: 197
红花: 48
沙发: 2
帖子: 2254
在线: 400.7小时
虫号: 1879241
注册: 2012-07-05
性别: GG
专业: 生物信息学

【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.

赞一下(1人)

回复此楼

3楼2015-01-11 10:13:12

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

yany19900707

铁虫 (初入文坛)

应助: 0 (幼儿园)
金币: 64.1
帖子: 31
在线: 24.5小时
虫号: 2729305
注册: 2013-10-16
性别: MM
专业: 系统生物学

请问楼主问题解决了吗？我的问题跟你一模一样

赞一下

回复此楼

NO.1

4楼2015-12-08 10:01:38

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

相关版块跳转我要订阅楼主小小的散的主题更新

返回列表

最具人气热帖推荐 [查看全部]		作者	回/看	最后发表

[考研] 0856，材料与化工321分求调剂 +7	大馋小子 2026-03-27	8/400	2026-03-27 22:31 by 无际的草原
[考研] 292求调剂 +13	鹅鹅鹅额额额额� 2026-03-25	14/700	2026-03-27 15:40 by caszguilin
[考研] 334求调剂 +3	雨清天晴 2026-03-21	3/150	2026-03-27 11:30 by 不吃魚的貓
[考研] 材料学硕333求调剂 +8	北道巷 2026-03-24	8/400	2026-03-27 10:18 by 我是小康
[考研] 359求调剂 +4	王了个楠 2026-03-25	4/200	2026-03-27 08:43 by 不吃魚的貓
[考研] 081200-11408-276学硕求调剂 +3	崔wj 2026-03-26	3/150	2026-03-27 07:58 by chemisry
[考研] 一志愿武汉理工，总分321，英一数二，求老师收留。 +5	nnnnnnn5 2026-03-25	5/250	2026-03-27 04:42 by wxiongid
[考研] 325求调剂 +5	李嘉图·S·路 2026-03-23	5/250	2026-03-27 00:42 by wxiongid
[考研] 351求调剂 +4	麦克阿磊 2026-03-24	4/200	2026-03-27 00:32 by wxiongid
[考研] 333求调剂 +6	wfh030413@ 2026-03-23	6/300	2026-03-26 22:45 by 学员8dgXkO
[考研] 一志愿北京化工大学材料与化工（085600）296求调剂 +9	稻妻小编 2026-03-26	9/450	2026-03-26 16:16 by 不吃魚的貓
[考研] 299求调剂 +7	某某某某位 2026-03-21	8/400	2026-03-25 20:34 by 热情沙漠
[考研] 求调剂 +3	李李不服输 2026-03-25	3/150	2026-03-25 13:03 by cmz0325
[考研] 282求调剂 +3	wcq131415 2026-03-24	3/150	2026-03-25 12:16 by userper
[考研] 300分，材料，求调剂，英一数二 +5	超赞的 2026-03-24	5/250	2026-03-24 21:07 by 星空星月
[考研] 求调剂一志愿武汉理工大学材料工程（085601） +5	WW.' 2026-03-23	7/350	2026-03-24 14:50 by sprinining
[考研] 085404电子信息284分求调剂 +4	13659058978 2026-03-24	4/200	2026-03-24 12:15 by syl20081243
[考研] 一志愿河北工业大学0817化工278分求调剂 +7	jhybd 2026-03-23	12/600	2026-03-24 09:03 by jhybd
[考研] 275求调剂 +6	shansx 2026-03-22	8/400	2026-03-22 15:27 by barlinike
[考研] 求调剂 +4	要好好无聊 2026-03-21	4/200	2026-03-21 18:57 by 学员8dgXkO

24小时热门版块排行榜

小小的散

[求助] 用pamlx做codeml的结果怎么分析？ 已有1人参与

» 猜你喜欢

小小的散

wizardfan

【答案】应助回帖

yany19900707

[求助] 用pamlx做codeml的结果怎么分析？已有1人参与