annotate test-data/3_run_codeml @ 0:961a712f9743 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8

CODONML (in paml version 4.9, March 2015)  /tmp/tmpMdbfK7/files/000/dataset_23.dat
Model: NSbranch3 for branches, 
Codon frequency model: F1x4
Site-class models:  PositiveSelection
ns =   6  ls = 13754

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT 232  13 253  68  16  40 | Ser TCT 276   5 291  78   8  58 | Tyr TAT  98   3  95  29   3  27 | Cys TGT 218   5 219  52  13  40
    TTC 251  14 308  87  34  71 |     TCC 227   8 241  55  15  49 |     TAC 126   7 151  37  18  25 |     TGC 150   3 155  45  11  34
Leu TTA 131   1 125  33   5  32 |     TCA 250   4 275  58  12  47 | *** TAA   0   0   0   0   0   0 | *** TGA   0   0   0   0   0   0
    TTG 245   6 291  67  18  42 |     TCG 104   6 106  19   7  16 |     TAG   0   0   0   0   0   0 | Trp TGG 168   9 195  28  18  27
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT 171   0 186  54   9  28 | Pro CCT 164   3 170  42  14  40 | His CAT 157   2 143  47  15  41 | Arg CGT  88   5  98  33  10  25
    CTC 147   9 160  47  20  35 |     CCC  81   6  95  16  17  18 |     CAC 137  10 158  42  21  32 |     CGC  57  16  58  16  29  39
    CTA  64   0  66  14   5  10 |     CCA 232  10 229  63  14  48 | Gln CAA 140   3 126  32  12  28 |     CGA  75  18  66  22  19  17
    CTG 249  18 261  55  25  43 |     CCG  65   9  63   6  19  19 |     CAG 192  19 213  53  25  51 |     CGG  51   4  58  17  12  11
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT 173   9 175  60   9  32 | Thr ACT 145   5 140  39   9  40 | Asn AAT 159   5 159  53  12  39 | Ser AGT 146   1 143  44   5  39
    ATC 218  27 238  54  36  50 |     ACC 123  18 154  62  12  36 |     AAC 184  17 188  65  26  36 |     AGC 160   6 185  36  14  40
    ATA 186   5 165  68   4  27 |     ACA 255   4 262  76  13  40 | Lys AAA 197  11 186  82  22  40 | Arg AGA 165   4 167  59   6  30
Met ATG 308  14 341  83  19  67 |     ACG  81   6 100  22   8  13 |     AAG 224  48 231  53  59  46 |     AGG 140  10 150  36  15  23
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT 176   8 185  40  17  30 | Ala GCT 184   5 184  51  15  40 | Asp GAT 182   5 189  64  15  54 | Gly GGT 160   7 140  40  16  34
    GTC 200  16 209  42  26  38 |     GCC 209  20 224  48  35  49 |     GAC 191  16 189  38  30  49 |     GGC 164  10 183  21  16  41
    GTA 166   3 149  50  14  23 |     GCA 183   4 176  58  17  34 | Glu GAA 148   6 152  58  16  40 |     GGA 163   7 155  35  19  26
    GTG 224  17 242  40  22  47 |     GCG  53  10  53  14  12  17 |     GAG 149  20 142  44  36  33 |     GGG  80   6  75   8   9  24
--------------------------------------------------------------------------------------------------------------------------------------

Codon position x base (3x4) table for each sequence.

#1: Ac             
position  1:    T:0.24656    C:0.20613    A:0.28520    G:0.26210
position  2:    T:0.31279    C:0.26210    A:0.22744    G:0.19767
position  3:    T:0.27176    C:0.26140    A:0.23452    G:0.23232
Average         T:0.27704    C:0.24321    A:0.24905    G:0.23070

#2: Am             
position  1:    T:0.14841    C:0.23322    A:0.33569    G:0.28269
position  2:    T:0.28269    C:0.21731    A:0.30389    G:0.19611
position  3:    T:0.14311    C:0.35866    A:0.14134    G:0.35689
Average         T:0.19140    C:0.26973    A:0.26031    G:0.27856

#3: Ap             
position  1:    T:0.25796    C:0.20504    A:0.28457    G:0.25243
position  2:    T:0.31986    C:0.26349    A:0.22144    G:0.19521
position  3:    T:0.26416    C:0.27618    A:0.21924    G:0.24042
Average         T:0.28066    C:0.24824    A:0.24175    G:0.22935

#4: Pg             
position  1:    T:0.23785    C:0.20268    A:0.32342    G:0.23604
position  2:    T:0.31255    C:0.25635    A:0.25272    G:0.17839
position  3:    T:0.28789    C:0.25780    A:0.25671    G:0.19761
Average         T:0.27943    C:0.23894    A:0.27762    G:0.20401

#5: Th             
position  1:    T:0.17315    C:0.25875    A:0.26167    G:0.30642
position  2:    T:0.27140    C:0.22082    A:0.30156    G:0.20623
position  3:    T:0.18093    C:0.35019    A:0.17315    G:0.29572
Average         T:0.20850    C:0.27659    A:0.24546    G:0.26946

#6: Ph             
position  1:    T:0.23410    C:0.22350    A:0.27558    G:0.26682
position  2:    T:0.28341    C:0.25991    A:0.24931    G:0.20737
position  3:    T:0.27972    C:0.29585    A:0.20369    G:0.22074
Average         T:0.26575    C:0.25975    A:0.24286    G:0.23164

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT     622 | Ser S TCT     716 | Tyr Y TAT     255 | Cys C TGT     547
      TTC     765 |       TCC     595 |       TAC     364 |       TGC     398
Leu L TTA     327 |       TCA     646 | *** * TAA       0 | *** * TGA       0
      TTG     669 |       TCG     258 |       TAG       0 | Trp W TGG     445
------------------------------------------------------------------------------
Leu L CTT     448 | Pro P CCT     433 | His H CAT     405 | Arg R CGT     259
      CTC     418 |       CCC     233 |       CAC     400 |       CGC     215
      CTA     159 |       CCA     596 | Gln Q CAA     341 |       CGA     217
      CTG     651 |       CCG     181 |       CAG     553 |       CGG     153
------------------------------------------------------------------------------
Ile I ATT     458 | Thr T ACT     378 | Asn N AAT     427 | Ser S AGT     378
      ATC     623 |       ACC     405 |       AAC     516 |       AGC     441
      ATA     455 |       ACA     650 | Lys K AAA     538 | Arg R AGA     431
Met M ATG     832 |       ACG     230 |       AAG     661 |       AGG     374
------------------------------------------------------------------------------
Val V GTT     456 | Ala A GCT     479 | Asp D GAT     509 | Gly G GGT     397
      GTC     531 |       GCC     585 |       GAC     513 |       GGC     435
      GTA     405 |       GCA     472 | Glu E GAA     420 |       GGA     405
      GTG     592 |       GCG     159 |       GAG     424 |       GGG     202
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.24425    C:0.20932    A:0.28824    G:0.25819
position  2:    T:0.31094    C:0.25937    A:0.23386    G:0.19582
position  3:    T:0.26495    C:0.27494    A:0.22410    G:0.23601
Average         T:0.27338    C:0.24787    A:0.24874    G:0.23001


Nei & Gojobori 1986. dN/dS (dN, dS)
(Pairwise deletion)
(Note: This matrix is not used in later ML. analysis.
Use runmode = -2 for ML pairwise comparison.)

Ac                  
Am                   0.0436 (0.0628 1.4398)
Ap                   0.4042 (0.0536 0.1327) 0.0340 (0.0422 1.2410)
Pg                   0.2101 (0.1215 0.5783)-1.0000 (0.0396 -1.0000) 0.3864 (0.1403 0.3631)
Th                   0.0067 (0.0137 2.0454)-1.0000 (0.0000 0.0066) 0.0930 (0.0932 1.0019) 0.0156 (0.0625 4.0052)
Ph                   0.1095 (0.0858 0.7837) 0.0387 (0.0613 1.5834) 0.2555 (0.1166 0.4563) 0.6800 (0.1673 0.2459)-1.0000 (-1.0000 -1.0000)
NOTE: -1 means that NG86 is inapplicable.


TREE #  1:  (((4, 2), 5), (6, 3), 1);   MP score: -1
lnL(ntime:  9  np: 15): -71845.285288      +0.000000
   7..8     8..9     9..4     9..2     8..5     7..10   10..6    10..3     7..1  
 0.253789 0.000004 0.294642 0.199868 0.242499 0.000004 0.471201 0.102634 0.122472 3.060446 0.693669 0.106076 0.279090 0.015724 0.820701

Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   1.68711

(((4: 0.294642, 2: 0.199868): 0.000004, 5: 0.242499): 0.253789, (6: 0.471201, 3: 0.102634): 0.000004, 1: 0.122472);

(((Pg: 0.294642, Am: 0.199868): 0.000004, Th: 0.242499): 0.253789, (Ph: 0.471201, Ap: 0.102634): 0.000004, Ac: 0.122472);

Detailed output identifying parameters

kappa (ts/tv) =  3.06045


MLEs of dN/dS (w) for site classes (K=3)

site class             0         1         2
proportion        0.69367   0.10608   0.20025
branch type 0:    0.27909   1.00000   0.01572
branch type 1:    0.27909   1.00000   0.82070


Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)

The grid (see ternary graph for p0-p1)

w0:   0.050  0.150  0.250  0.350  0.450  0.550  0.650  0.750  0.850  0.950
w2:   0.150  0.450  0.750  1.050  1.350  1.650  1.950  2.250  2.550  2.850
w3:   0.150  0.450  0.750  1.050  1.350  1.650  1.950  2.250  2.550  2.850


Posterior on the grid

w0:   0.000  0.016  0.738  0.171  0.066  0.006  0.002  0.000  0.000  0.000
w2:   0.988  0.012  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w3:   0.000  0.828  0.064  0.033  0.057  0.014  0.001  0.001  0.000  0.001

Posterior for p0-p1 (see the ternary graph) (YWN2015, fig. 1)

 0.000
 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.001 0.001 0.010 0.010 0.072 0.038 0.202 0.053 0.170 0.020 0.034 0.002 0.046 0.000 0.006 0.000 0.000
 0.000 0.000 0.000 0.003 0.004 0.039 0.014 0.031 0.010 0.101 0.007 0.020 0.001 0.026 0.001 0.072 0.003 0.001 0.000

sum of density on p0-p1 =   1.000000

Time used:  4:22