      3   1008

orangutan                       ATG AGG AGA CCC AGG GCC CAG CTG ATT TTC TGT GTC ACA AAG GGA AAT AAT CTA CCT GCT GTG ACA GAA CCA AGG CCA GAA CAC AGC AGA ATG GGG CCC CCC TCA GCT CGT CCC CAC AGA GAA TGC ATC CCC TGG CAG GGG CTC CTG CTC ACA GCC TCA CTT TTA ACC TTC TGG AAC GCG CCC ACC ACT GCC AGG CTC TTT ATT GTA TCA GTG CCC TTT GAA GTT GCT GAA GGG GAG AAT GTT CAT CTC TCT GTG GTT TAT CTG CCC GAG AAT CTT TAC AGC TAT GGC TGG TAC AAA GGG AAA ACG GTG GAG CCC AAC CAG CTA ATC GCA GCA TAT GTA ATA GAC ACT CAC GTT AGG ACT CCA GGG CCT GCA TAC AGC GGT CGA GAG ACA ATA TCA CCC AGT GGA GAT CTG CAT TTC CAG AAC GTC ACC CTG GAG GAC ACG GGA TAC TAC ACC CTA CAA GTC ACA TAC AGA AAT TCT CAG ATT GAC CAG GCA TCT CAC CAT CTC CGT GTA TAC ATG GCC CCA AGA CAC TTT CTG TTG GTC ACT CTA TCC ACA GAG TCA GTG GCT CAG CCC TCC ATC CAA GCC AGC AGC ACC ACA GTC ACA GAG AAG GGC TCT GTG GTC CTG ACC TGC CAC ACA AAT AAC ACT GGA ACC TCT TTC CAG CGG ATT TTC AAT AAC CAG AGT CTG CAG GTC ACG AAG AGG ATG GCG CTG TCC TGG TTT AAC CAT GTG CTC ACC ATA GAC CCC ATC AGG CAG GAG GAT GCT GGG GAG TAT CAG TGT GAG GTC TCC AAC CCA GTC AGC TCC AAC AGG AGT GAC CCC CTC AAG CTG ACT GTA AAA TCA GAT GAT AAC ACC CTA GGC ATC CTG ATC GGG GTC CTG GTT GGG AAT CTT CTG GTG GCT GCA CTG GTG TGT TTC CTG CTC CTC CGA AAA GCT GGC AGG GCC AGT GAT CAG AGT GAC TTC AGA GAG CAG CAG CCC TCA GCC TCC ACC CCC GGC CAC GGA CCC TCT GAC AGC TCC ATC TCC 
human                           ATG AGG AGA CCC AGG GCC CAG CTG GTT TTG TGT GTC ACA AAG GGA AAT AAT CTA CCG GCT GTG ACA GAA CCA AGG CCA GAA CAC AGC AGA ATG GGG CCC CCC TCA GCT TGT CCC CAC AGA GAA TGC ATC CCC TGG CAG GGG CTC TTG CTC ACA GCC TCA CTT TTA ACT TTC TGG AAC GCA CCC ACC ACT GCC TGG CTC TTT ATT GCA TCA GCG CCC TTT GAA GTT GCT GAA GGG GAG AAT GTT CAT CTC TCT GTG GTT TAT CTG CCC GAG AAT CTT TAC AGC TAT GGC TGG TAC AAA GGG AAA ACG GTG GAG CCC AAC CAG CTA ATC GCA GCA TAT GTA ATA GAC ACT CAC GTT AGG ACT CCA GGG CCT GCA TAC AGC GGT CGA GAG ACA ATA TCA CCC AGT GGA GAT CTG CAT TTC CAG AAC GTC ACC CTA GAG GAC ACG GGA TAC TAC AAC CTA CAA GTC ACA TAC AGA AAT TCT CAG ATT GAA CAG GCA TCT CAC CAT CTC CGT GTA TAC ATG GCC CCA AGA CAC TTT CTG TTG GTC ACT CTA TCC ACA GAG TCA GTG GCT CAG CCC TCC ATC CAA GCC AGC AGC ACC ACA GTC ACA GAG AAG GGC TCC GTG GTC CTG ACC TGC CAC ACA AAT AAC ACT GGA ACC TCT TTC CAG TGG ATT TTC AAC AAC CAG CGT CTG CAG GTC ACG AAG AGG ATG AAG CTG TCC TGG TTT AAC CAT GTG CTC ACC ATA GAC CCC ATC AGG CAG GAG GAC GCT GGG GAG TAT CAG TGT GAG GTC TCC AAC CCA GTC AGC TCC AAC AGG AGC GAC CCC CTC AAG CTG ACT GTA AAA TCA GAT GAC AAC ACT CTA GGC ATC CTG ATC GGG GTC CTG GTT GGG AGT CTT CTG GTG GCT GCA CTT GTG TGT TTC CTG CTC CTC CGA AAA ACT GGC AGG GCC AGC GAT CAG AGT GAC TTC AGG GAG CAG CAG CCC CCA GCC TCC ACC CCC GGC CAT GGA CCC TCT GAC AGC TCC ATC TCC 
gorilla                         ATG AGG AGA CCC AGG GCC CAG CCG GTT TTC TGT GTC ACA AAG GGA AAT AAT CTA CCT GCT GTG ACA GAA CCA AGG CCA GAA CAC AGC AGA ATG GGG CCC CCC TCA GCT CGT CCC CAC AGA GAA TGC ATC CCC TGG CAG GGG CTC TTG CTC ATA GCC TCA CTT TTA ACC TTC TGG AAC GCA CCC ACC ACT GCC TGG CTC TTT ATT GCA TCA GCG CCC TTT GAA GTT GCT GAA GGG GAG AAT GTT CAT CTC TCT GTG GTT TAT CTG CCC GAG AAT CTT TAC AGC TAT GGC TGG TAC AAA GGG AAA ACA GTG GAG CCC AAC CAG CTA ATC GCA GCA TAT GTA ACA GAC ACT CAC GTT AGG ACT CCA GGG CCT GCA TAC AGC GGT CGA GAA ACA ATA TCA CCC AGT GGA GAT CTG CAT TTC CAG AAC GTC ACC CTG GAG GAC ACG GGA TAC TAC ACC CTA CAA GTC AGA TAC AGA AAT TCT CAG ATT GAA CAG GCA TCT CAC CAT CTC CGT GTA TAC ATG GCC CCA AGA CAC TTT CTG TTG GTC ACT CTA TCC ACA GAG TCA GTG GCT CAG CCC TCC ATC CAA GCC AGC AGC ACC ACA GTC ACA GAG AAG GGC TCC GTG GTC CTG ACC TGC CGC ACA AAT AAC ACT GGA ACC TCT TTC CAG TGG ATT TTC AAC AAC CAG CGT CTG CAG GTC ACG AAG AGG ATG AAG CTG TCC TGG TTT AAC CAT ATG CTC ACC ATA GAC CCA ATC AGG CAG GAG GAC GCC GGG GAG TAT CAG TGT GAG GTC TCC AAC CCA GTC AGC TCC AAC AGG AGT GAC CCC CTC AAG CTG ACT GTA AAA TCA GAT GAC AAC ACC CTA GGC ATC CTG ATC GGG GTC CTG GTT GGG AGT CTT CTG GTG GCT GCA CTT GTG TGT TTC CTG CTC CTC CGA AAA ACT GGC AGG GCC AGC GAT CAG AGT GAC TTC AGG GAG CAG CAG CCC CCA GCC TCC ACC CCT GGC CAT GGA CCC TCT GAC AGC TCC ATC TCC 



Printing out site pattern counts


         3        282  P

orangutan                       AAA AAC AAG AAT AAT AAT ACA ACA ACA ACC ACC ACC ACG ACG ACT AGA AGA AGC AGG AGG AGT AGT AGT AGT ATA ATA ATC ATG ATT ATT CAA CAC CAC CAC CAG CAT CCA CCC CCC CCC CCT CCT CGA CGG CGT CGT CTA CTC CTG CTG CTG CTG CTG CTT GAA GAC GAC GAG GAG GAT GAT GCA GCC GCG GCG GCT GCT GCT GGA GGC GGG GGT GTA GTA GTC GTG GTG GTG GTT TAC TAT TCA TCA TCC TCT TCT TGC TGG TGT TTA TTC TTC TTG TTT 
human                           ... ... ... ..C ... .G. ... ... ... .A. ... ..T ... ... ... ... ..G ... ... T.. ..C ..C ... C.. ... ... ... ... ... G.. ... ... ... ..T ... ... ... ... ... ... ..G ... ... T.. ... T.. ... ... ..A ... ... ..T T.. ... ... ..A ... ... ... ..C ... ... ... AA. ..A A.. ... ... ... ... ... ... .C. ... ... .C. ... ... ... ... ... C.. ... ... ..C ... ... ... ... ... ... ..G ... ... 
gorilla                         ... ... ... ..C ... .G. ... .G. .T. ... ... ... ..A ... ... ... ..G ... ... T.. ..C ... ... C.. .C. ... ... ... ... G.. ... ... .G. ..T ... ... ... ..A ... ..T ... ... ... T.. ... ... ... ... ... .C. ... ..T T.. ... ... ..A ... ..A ... ..C ... ... ... AA. ..A A.. ..C ... ... ... ... ... .C. ... ... .C. A.. ... ... ... ... C.. ... ... ..C ... ... ... ... ... ... ... ... ... 

    4    9    4    1    6    1    7    1    1    1    7    2    1    2    6
    5    1    7    8    1    1    1    2    1    1    2    7    4    3    1
    2    5    1    1   15    4    5    1   14    1    1    1    2    1    1
    1    5    9    1    1   11    1    1    3    5    1    6    1   10    2
    3    5    7    1    1    1    1    5    5    5    8    1    1    3   10
    1    1    7    5    7    4    1    6    8    1    5    2    4    3    1
    6    1    1    4

CODONML (in paml version 4.9h, March 2018)  CEACAM21seq.fasta
Model: One dN/dS ratio, 
Codon frequency model: F3x4
Site-class models: 
ns =   3  ls = 336

Codon usage in sequences
--------------------------------------------------------------------------------------
Phe TTT   4   4   4 | Ser TCT   6   5   5 | Tyr TAT   4   4   4 | Cys TGT   3   4   3
    TTC   7   6   7 |     TCC   8   9   9 |     TAC   7   7   7 |     TGC   2   2   2
Leu TTA   1   1   1 |     TCA   7   6   6 | *** TAA   0   0   0 | *** TGA   0   0   0
    TTG   1   3   2 |     TCG   0   0   0 |     TAG   0   0   0 | Trp TGG   4   6   6
--------------------------------------------------------------------------------------
Leu CTT   3   4   4 | Pro CCT   2   1   3 | His CAT   4   5   5 | Arg CGT   2   2   3
    CTC   9   9   9 |     CCC  16  16  14 |     CAC   7   6   5 |     CGC   0   0   1
    CTA   5   6   5 |     CCA   5   6   7 | Gln CAA   2   2   2 |     CGA   2   2   2
    CTG  15  12  12 |     CCG   0   1   1 |     CAG  15  15  15 |     CGG   1   0   0
--------------------------------------------------------------------------------------
Ile ATT   4   3   3 | Thr ACT   6   9   7 | Asn AAT   8   6   6 | Ser AGT   5   3   4
    ATC   7   7   7 |     ACC  10   7  10 |     AAC   9  11  10 |     AGC   7   9   8
    ATA   3   3   3 |     ACA   9   9   9 | Lys AAA   4   4   4 | Arg AGA   6   5   6
Met ATG   4   4   5 |     ACG   3   3   2 |     AAG   4   5   5 |     AGG   9   9   9
--------------------------------------------------------------------------------------
Val GTT   5   6   6 | Ala GCT   7   6   5 | Asp GAT   5   3   3 | Gly GGT   1   1   1
    GTC  10  10  10 |     GCC   7   7   8 |     GAC   7   8   8 |     GGC   5   5   5
    GTA   4   3   3 |     GCA   5   7   7 | Glu GAA   5   6   7 |     GGA   5   5   5
    GTG   9   8   7 |     GCG   2   1   1 |     GAG  11  11  10 |     GGG   8   8   8
--------------------------------------------------------------------------------------

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

#1: orangutan      
position  1:    T:0.16071    C:0.26190    A:0.29167    G:0.28571
position  2:    T:0.27083    C:0.27679    A:0.27381    G:0.17857
position  3:    T:0.20536    C:0.35119    A:0.18750    G:0.25595
Average         T:0.21230    C:0.29663    A:0.25099    G:0.24008

#2: human          
position  1:    T:0.16964    C:0.25893    A:0.28869    G:0.28274
position  2:    T:0.26488    C:0.27679    A:0.27679    G:0.18155
position  3:    T:0.19643    C:0.35417    A:0.19345    G:0.25595
Average         T:0.21032    C:0.29663    A:0.25298    G:0.24008

#3: gorilla        
position  1:    T:0.16667    C:0.26190    A:0.29167    G:0.27976
position  2:    T:0.26190    C:0.27976    A:0.27083    G:0.18750
position  3:    T:0.19643    C:0.35714    A:0.19940    G:0.24702
Average         T:0.20833    C:0.29960    A:0.25397    G:0.23810

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      12 | Ser S TCT      16 | Tyr Y TAT      12 | Cys C TGT      10
      TTC      20 |       TCC      26 |       TAC      21 |       TGC       6
Leu L TTA       3 |       TCA      19 | *** * TAA       0 | *** * TGA       0
      TTG       6 |       TCG       0 |       TAG       0 | Trp W TGG      16
------------------------------------------------------------------------------
Leu L CTT      11 | Pro P CCT       6 | His H CAT      14 | Arg R CGT       7
      CTC      27 |       CCC      46 |       CAC      18 |       CGC       1
      CTA      16 |       CCA      18 | Gln Q CAA       6 |       CGA       6
      CTG      39 |       CCG       2 |       CAG      45 |       CGG       1
------------------------------------------------------------------------------
Ile I ATT      10 | Thr T ACT      22 | Asn N AAT      20 | Ser S AGT      12
      ATC      21 |       ACC      27 |       AAC      30 |       AGC      24
      ATA       9 |       ACA      27 | Lys K AAA      12 | Arg R AGA      17
Met M ATG      13 |       ACG       8 |       AAG      14 |       AGG      27
------------------------------------------------------------------------------
Val V GTT      17 | Ala A GCT      18 | Asp D GAT      11 | Gly G GGT       3
      GTC      30 |       GCC      22 |       GAC      23 |       GGC      15
      GTA      10 |       GCA      19 | Glu E GAA      18 |       GGA      15
      GTG      24 |       GCG       4 |       GAG      32 |       GGG      24
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.16567    C:0.26091    A:0.29067    G:0.28274
position  2:    T:0.26587    C:0.27778    A:0.27381    G:0.18254
position  3:    T:0.19940    C:0.35417    A:0.19345    G:0.25298
Average         T:0.21032    C:0.29762    A:0.25265    G:0.23942

Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
  0.00901887  0.01601859  0.00874965  0.01144185
  0.00942270  0.01673584  0.00914143  0.01195417
  0.00928809  0.01649676  0.00000000  0.00000000
  0.00619206  0.01099784  0.00000000  0.00785560
  0.01420337  0.02522689  0.01377939  0.01801920
  0.01483934  0.02635645  0.01439638  0.01882603
  0.01462735  0.02597993  0.01419072  0.01855709
  0.00975157  0.01731995  0.00946048  0.01237139
  0.01582353  0.02810448  0.01535119  0.02007463
  0.01653205  0.02936289  0.01603855  0.02097349
  0.01629587  0.02894342  0.01580943  0.02067387
  0.01086392  0.01929561  0.01053962  0.01378258
  0.01539149  0.02733712  0.01493204  0.01952651
  0.01608066  0.02856117  0.01560064  0.02040084
  0.01585093  0.02815315  0.01537777  0.02010939
  0.01056729  0.01876877  0.01025185  0.01340626


Model 1: NearlyNeutral (2 categories)


TREE #  1:  ((2, 3), 1);   MP score: 40
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  7):  -1606.242481      +0.000000
   4..5     5..2     5..3     4..1  
 0.052196 0.024960 0.034399 0.017880 5.600371 0.578591 0.000001

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

tree length =  0.129436

((2: 0.024960, 3: 0.034399): 0.052196, 1: 0.017880);

((human: 0.024960, gorilla: 0.034399): 0.052196, orangutan: 0.017880);

Detailed output identifying parameters

kappa (ts/tv) =  5.60037


MLEs of dN/dS (w) for site classes (K=2)

p:   0.57859  0.42141
w:   0.00000  1.00000

dN & dS for each branch

 branch          t       N       S   dN/dS      dN      dS  N*dN  S*dS

   4..5       0.052    716.8    291.2   0.4214   0.0125   0.0296    8.9    8.6
   5..2       0.025    716.8    291.2   0.4214   0.0060   0.0141    4.3    4.1
   5..3       0.034    716.8    291.2   0.4214   0.0082   0.0195    5.9    5.7
   4..1       0.018    716.8    291.2   0.4214   0.0043   0.0101    3.1    2.9


Time used:  0:01


Model 2: PositiveSelection (3 categories)


TREE #  1:  ((2, 3), 1);   MP score: 40
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1606.165665      +0.000000
   4..5     5..2     5..3     4..1  
 0.043153 0.025418 0.034676 0.028014 5.673816 0.703482 0.000000 0.000001 1.512860

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

tree length =  0.131261

((2: 0.025418, 3: 0.034676): 0.043153, 1: 0.028014);

((human: 0.025418, gorilla: 0.034676): 0.043153, orangutan: 0.028014);

Detailed output identifying parameters

kappa (ts/tv) =  5.67382


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

p:   0.70348  0.00000  0.29652
w:   0.00000  1.00000  1.51286

dN & dS for each branch

 branch          t       N       S   dN/dS      dN      dS  N*dN  S*dS

   4..5       0.043    716.5    291.5   0.4486   0.0106   0.0237    7.6    6.9
   5..2       0.025    716.5    291.5   0.4486   0.0063   0.0139    4.5    4.1
   5..3       0.035    716.5    291.5   0.4486   0.0085   0.0190    6.1    5.5
   4..1       0.028    716.5    291.5   0.4486   0.0069   0.0154    4.9    4.5


Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: orangutan)

            Pr(w>1)     post mean +- SE for w

     8 L      1.000**       1.513
     9 I      1.000**       1.513
    10 F      1.000**       1.513
    37 R      1.000**       1.513
    51 T      1.000**       1.513
    65 R      1.000**       1.513
    69 V      1.000**       1.513
    71 V      1.000**       1.513
   114 I      1.000**       1.513
   151 T      1.000**       1.513
   155 T      1.000**       1.513
   162 D      1.000**       1.513
   210 H      1.000**       1.513
   220 R      1.000**       1.513
   226 S      1.000**       1.513
   234 A      1.000**       1.513
   241 V      1.000**       1.513
   292 N      1.000**       1.513
   307 A      1.000**       1.513
   322 S      1.000**       1.513


Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: orangutan)

            Pr(w>1)     post mean +- SE for w

   234 A      0.657         3.127 +- 2.637



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:   1.500  2.500  3.500  4.500  5.500  6.500  7.500  8.500  9.500 10.500


Posterior on the grid

w0:   0.320  0.293  0.221  0.115  0.039  0.009  0.002  0.000  0.000  0.000
w2:   0.290  0.186  0.137  0.106  0.082  0.064  0.049  0.037  0.028  0.021

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 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.009
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.006 0.035
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.007 0.023 0.089
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.008 0.019 0.054 0.132
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.004 0.010 0.019 0.035 0.082 0.132
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.006 0.011 0.020 0.031 0.047 0.087 0.119

sum of density on p0-p1 =   1.000000

Time used:  0:09


Model 7: beta (10 categories)


TREE #  1:  ((2, 3), 1);   MP score: 40
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  7):  -1606.255277      +0.000000
   4..5     5..2     5..3     4..1  
 0.029314 0.024935 0.034381 0.040716 5.572431 0.011512 0.014944

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

tree length =  0.129346

((2: 0.024935, 3: 0.034381): 0.029314, 1: 0.040716);

((human: 0.024935, gorilla: 0.034381): 0.029314, orangutan: 0.040716);

Detailed output identifying parameters

kappa (ts/tv) =  5.57243

Parameters in M7 (beta):
 p =   0.01151  q =   0.01494


MLEs of dN/dS (w) for site classes (K=10)

p:   0.10000  0.10000  0.10000  0.10000  0.10000  0.10000  0.10000  0.10000  0.10000  0.10000
w:   0.00000  0.00000  0.00000  0.00000  0.00000  0.08807  1.00000  1.00000  1.00000  1.00000

dN & dS for each branch

 branch          t       N       S   dN/dS      dN      dS  N*dN  S*dS

   4..5       0.029    716.9    291.1   0.4088   0.0069   0.0169    4.9    4.9
   5..2       0.025    716.9    291.1   0.4088   0.0059   0.0143    4.2    4.2
   5..3       0.034    716.9    291.1   0.4088   0.0081   0.0198    5.8    5.8
   4..1       0.041    716.9    291.1   0.4088   0.0096   0.0234    6.9    6.8


Time used:  0:37


Model 8: beta&w>1 (11 categories)


TREE #  1:  ((2, 3), 1);   MP score: 40
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1606.165665      +0.000000
   4..5     5..2     5..3     4..1  
 0.000004 0.025418 0.034677 0.071163 5.673817 0.703482 0.005000 2.520408 1.512861

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

tree length =  0.131261

((2: 0.025418, 3: 0.034677): 0.000004, 1: 0.071163);

((human: 0.025418, gorilla: 0.034677): 0.000004, orangutan: 0.071163);

Detailed output identifying parameters

kappa (ts/tv) =  5.67382

Parameters in M8 (beta&w>1):
  p0 =   0.70348  p =   0.00500 q =   2.52041
 (p1 =   0.29652) w =   1.51286


MLEs of dN/dS (w) for site classes (K=11)

p:   0.07035  0.07035  0.07035  0.07035  0.07035  0.07035  0.07035  0.07035  0.07035  0.07035  0.29652
w:   0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  0.00001  1.51286

dN & dS for each branch

 branch          t       N       S   dN/dS      dN      dS  N*dN  S*dS

   4..5       0.000    716.5    291.5   0.4486   0.0000   0.0000    0.0    0.0
   5..2       0.025    716.5    291.5   0.4486   0.0063   0.0139    4.5    4.1
   5..3       0.035    716.5    291.5   0.4486   0.0085   0.0190    6.1    5.5
   4..1       0.071    716.5    291.5   0.4486   0.0175   0.0390   12.5   11.4


Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: orangutan)

            Pr(w>1)     post mean +- SE for w

     8 L      1.000**       1.513
     9 I      1.000**       1.513
    10 F      1.000**       1.513
    37 R      1.000**       1.513
    51 T      1.000**       1.513
    65 R      1.000**       1.513
    69 V      1.000**       1.513
    71 V      1.000**       1.513
   114 I      1.000**       1.513
   151 T      1.000**       1.513
   155 T      1.000**       1.513
   162 D      1.000**       1.513
   210 H      1.000**       1.513
   220 R      1.000**       1.513
   226 S      1.000**       1.513
   234 A      1.000**       1.513
   241 V      1.000**       1.513
   292 N      1.000**       1.513
   307 A      1.000**       1.513
   322 S      1.000**       1.513


Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: orangutan)

            Pr(w>1)     post mean +- SE for w

   234 A      0.739         3.077 +- 2.473



The grid 

p0:   0.050  0.150  0.250  0.350  0.450  0.550  0.650  0.750  0.850  0.950
p :   0.100  0.300  0.500  0.700  0.900  1.100  1.300  1.500  1.700  1.900
q :   0.100  0.300  0.500  0.700  0.900  1.100  1.300  1.500  1.700  1.900
ws:   1.500  2.500  3.500  4.500  5.500  6.500  7.500  8.500  9.500 10.500


Posterior on the grid

p0:   0.000  0.000  0.000  0.000  0.000  0.002  0.018  0.078  0.212  0.689
p :   0.199  0.217  0.188  0.141  0.097  0.063  0.041  0.026  0.017  0.011
q :   0.006  0.037  0.053  0.073  0.093  0.112  0.131  0.149  0.166  0.181
ws:   0.318  0.197  0.139  0.105  0.080  0.059  0.042  0.029  0.019  0.013

Time used:  1:04
