
seed used = 727954689
      6    402

PITG_23265T0                               ATG AAA TCG CAA GCT TTC GCC CAG GAG GAA CCT GTG CTA TGG ACG GAT ATA CAT CAT GGG GCA CGC TTT GGC GAT GGA TGC AAT CGA CGC GTT ATT GAG CGG CAA TTG ACG TAT GCG CTT GCT GAC AAG CGA ATG CCA ACG AAG ACC AAA GGA TTT CAG AAA GGA AGG TGC TCT TGC GGT AAT GAT CAA GGG AAG TGC TTT CTG TAT CAA TCT GTA GAC GCG TCT CCG TCT AGT GAT GCA TTT CTG TGT CTG GAA GAT GCG ACG AAG GGC TTC TTT CAC GAG GTT CAT CAG TGT AAG TGT GAC GAA GGG AAT CTA TCA CTG GAC GTT TCC AAG CAA GAG CGG TCG AAG GCT GCT ACC --- --- --- --- TAT TCA TTT TGT ATT GCA CGA GTC AGG --- --- 
PITG_23253T0                               --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ATG ATT CAT GGG GCA CGG GTT GGC GAT GGA TGC AAT CGA CGC GAT ATT GAG CGG CAA TTG ACG TAT GCG CTA GCT GAC AAG CGG ATG CCA ACG AAG ACC AAA GGA TTT AAG AAA GAA AGG TGC TCT TGC GGT AAT GAT CAA GGG AAG TGT TTT CTG TAT CAG CCT GCA GAC GGG TCT CCG TCC GAA GAT GCA TTT CTG TGT CTG GAA GAT GCG ACG AAG GGC TTC TTT CAC GAG GTT CAT CAG TGT AAA TGC GTC GAA GGG AAT CTA TCA CTG GAC GTT TTC GAG CAA GAG CGG TTA AGG CTG CTG GTC CCG --- ACG ACC TAT TCA TCT TAT ATT GCA CGA GCC --- --- --- 
PITG_23257T0                               --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ATG CGC TTG CTG ACA AGC GGA --- --- --- --- --- TGC CAA CGA AGA CCC AAG GAT TTA AAG AAA AGA AGG TGC TCT TGC GGT AAT GAT CAA GGG AAG TGT TTT CTG TAT CAG CCT GCA GAC GGG CCT CCA TCC GGA GAT GCA TTT CTG TGT CTG GAA GAT GCG ACG AAG GGC TTC TTT CAC GAG GTT CAT CAG TGT AAA TGC GTC GAA GGG AAT CTA TCA CTG GAC GTT TTC GAG CAA GAG CGG TTG AAG GCT GCT GGA CCT --- --- --- ATT CAT CTT ATA TTG CAC GAG CCT AGT GAC GGT 
PITG_23264T0                               --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ATG CCA ACG AAG ACC AAA GGA TTT CAG AAA GGA AGG TGC TCT TGC GGT AAT GAT CAA GGA AAG TGC TTT CTG TAT CAA TCT GCA GAC GGG TCT CCG TTC GGA GAT GCA TTT CTG TGT CTG GAA GAT GCG ACG AAG GGC TTC TTT CAC GAG GTT CAT CAG TGT AAA TGC GTC GAA GGG AAT CTA TCA CTG GAC GTT TTC AAG CAA GAG CGG TCG AAG GCT GCT GGT CCC GAC GAC CTA TTC ATC TTG TGT TGC ACG AGC CCA AGT GAC GGC 
PITG_23267T0                               --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ATG CCA ACG AAG ACC AAA GGA TTT CAG AAA GGA AGG TGC TCT TGC GGT AAT GAT CAA GGG AAG TGC TTT CTG TAT CAA TCT GTA GAC GCG TCT CCG TCT AGT GAT GCA TTT CTG TGT CTG GAA GAT GCG ACG AAG GGC TTC TTT CAC GAG GTT CAT CAG TGT AAG TGT GAC GAA GGG AAT CTA TCA CTG GAC GTT TCC AAG CAA GAG CGG TCG AAG GCT GCT ACC --- --- --- --- TAT TCA TTT TGT ATT GCA CGA GTC AAG --- --- 
PITG_23293T0                               --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ATG CCA ACG AAG ACC AAA GGA TTT CAG AAA GGA AGG TGC TCT TGC GGT AAT GAT CAA GGG AAG TGC TTT CTG TAT CAA TCT GTA GAC GCG TCT CCG TCT AGT GAT GCA TTT CTG TGT CTG GAA GAT GCG ACG AAG GGC TTC TTT CAC GAG GTT CAT CAG TGT AAG TGC GAC GAA GGG AAT CTA TCA CTG TCA GAC TCC --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- 



Printing out site pattern counts


         6        363  P

PITG_23265T0                               --- --- --- --- --- --- AAA AAA AAA AAG AAG AAG AAG AAG AAG AAT AAT ACC ACC ACG ACG ACG ACG AGG AGG AGT ATA ATG ATG ATT ATT CAA CAA CAA CAA CAA CAC CAG CAG CAG CAT CAT CAT CCA CCG CCT CGA CGA CGA CGC CGC CGG CGG CTA CTA CTG CTT GAA GAA GAC GAC GAC GAC GAG GAG GAG GAG GAT GAT GAT GCA GCA GCA GCC GCG GCG GCG GCT GCT GCT GGA GGA GGA GGC GGC GGG GGG GGG GGT GTA GTC GTG GTT GTT GTT TAT TAT TAT TCA TCA TCC TCG TCG TCT TCT TCT TCT TGC TGC TGC TGG TGT TGT TGT TTC TTC TTG TTT TTT TTT TTT 
PITG_23253T0                               --- --- --- ACC ACG CCG --- AAA AAA AAA AAG AAG AAG AGG GAG AAT AAT ACC GTC --- ACG ACG ACG --- AGG GAA ATG --- ATG ATT ATT --- CAA CAA CAA CAG CAC --- AAG CAG ATT CAT CAT CCA CCG --- CGA CGA CGG CGC CGG CGG CGG --- CTA CTG CTA --- GAA GAC GAC GAC GTC --- GAG GAG GAG --- GAT GAT GCA GCA GCA --- GCG GCG GGG --- CTG GCT GAA GGA GGA GGC GGC GGG GGG GGG GGT GCA GCC --- GAT GTT GTT TAT TAT TAT TCA TCA TTC --- TTA CCT TCC TCT TCT TGC TGC TGT --- TAT TGC TGT --- TTC TTG GTT TCT TTT TTT 
PITG_23257T0                               --- GAC GGT --- --- CCT --- AAA AAG AAA --- AAG AGA AAG GAG --- AAT CCC GGA --- ACA ACG CGA AGT AGG GGA --- --- TGC --- TTG --- CAA CAA TTG CAG CAC --- AAG CAG --- --- CAT CAA CCA --- --- GAG --- --- --- CGC CGG --- CTA CTG --- --- GAA --- GAC GAC GTC --- ATG GAG GAG --- --- GAT --- CAC GCA --- GCG GGA GGG --- GCT --- AGA --- GAT --- GGC --- GGG GGG GGT GCA CCT --- --- GTT GTT AGC ATT TAT CAT TCA TTC --- TTG CCT TCC CCT TCT --- TGC TGT --- ATA TGC TGT --- TTC CTG --- CTT TTA TTT 
PITG_23264T0                               GAC GAC GGC CTA GAC CCC --- AAA AAA AAA --- AAG AAG AAG AAG --- AAT ACC GGT --- --- ACG ACG AGT AGG GGA --- --- ATG --- TGC --- CAA CAA --- CAA CAC --- CAG CAG --- --- CAT CCA CCG --- --- AGC --- --- --- --- CGG --- CTA CTG --- --- GAA --- GAC GAC GTC --- --- GAG GAG --- --- GAT --- ACG GCA --- GCG --- GGG --- GCT --- GGA --- GGA --- GGC --- GGA GGG GGT GCA CCA --- --- GTT GTT --- TTC TAT ATC TCA TTC --- TCG TCT TTC TCT TCT --- TGC TGC --- TGT TGC TGT --- TTC --- --- TTG TTT TTT 
PITG_23267T0                               --- --- --- --- --- --- --- AAA AAA AAG --- AAG AAG AAG AAG --- AAT ACC ACC --- --- ACG ACG AAG AGG AGT --- --- ATG --- ATT --- CAA CAA --- CAA CAC --- CAG CAG --- --- CAT CCA CCG --- --- CGA --- --- --- --- CGG --- CTA CTG --- --- GAA --- GAC GAC GAC --- --- GAG GAG --- --- GAT --- GCA GCA --- GCG --- GCG --- GCT --- GGA --- GGA --- GGC --- GGG GGG GGT GTA GTC --- --- GTT GTT --- TAT TAT TCA TCA TCC --- TCG TCT TCT TCT TCT --- TGC TGC --- TGT TGT TGT --- TTC --- --- TTT TTT TTT 
PITG_23293T0                               --- --- --- --- --- --- --- AAA AAA AAG --- AAG AAG --- --- --- AAT ACC --- --- --- ACG ACG --- AGG AGT --- --- ATG --- --- --- --- CAA --- CAA CAC --- CAG CAG --- --- CAT CCA CCG --- --- --- --- --- --- --- --- --- CTA CTG --- --- GAA --- GAC TCA GAC --- --- --- GAG --- --- GAT --- --- GCA --- GCG --- GCG --- --- --- GGA --- GGA --- GGC --- GGG GGG GGT GTA --- --- --- GAC GTT --- --- TAT --- TCA TCC --- --- TCT TCT TCT TCT --- TGC TGC --- --- TGC TGT --- TTC --- --- --- TTT TTT 



    1    1    1    1    1    1    1    1    1    1    1    2    1    1    1
    1    2    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    4    1    1    2    1
    1    1    1    1    1    1    1    1    1    3    1    1    1    1    1
    1    1    1    2    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    2    1    1    1    1    2    1    1    1    1    1    1
    3

CODONML (in paml version 4.3, August 2009)  alignment.phy
Model: One dN/dS ratio for branches
Codon frequency model: F3x4
Site-class models: 
ns =   6  ls = 134

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

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

#1: PITG_23265T0   
position  1:    T:0.23438    C:0.22656    A:0.21094    G:0.32812
position  2:    T:0.21094    C:0.22656    A:0.34375    G:0.21875
position  3:    T:0.32031    C:0.15625    A:0.21094    G:0.31250
Average         T:0.25521    C:0.20312    A:0.25521    G:0.28646

#2: PITG_23253T0   
position  1:    T:0.21930    C:0.23684    A:0.21053    G:0.33333
position  2:    T:0.22807    C:0.21053    A:0.34211    G:0.21930
position  3:    T:0.28947    C:0.16667    A:0.21053    G:0.33333
Average         T:0.24561    C:0.20468    A:0.25439    G:0.29532

#3: PITG_23257T0   
position  1:    T:0.21277    C:0.26596    A:0.20213    G:0.31915
position  2:    T:0.23404    C:0.17021    A:0.34043    G:0.25532
position  3:    T:0.30851    C:0.18085    A:0.22340    G:0.28723
Average         T:0.25177    C:0.20567    A:0.25532    G:0.28723

#4: PITG_23264T0   
position  1:    T:0.25556    C:0.20000    A:0.21111    G:0.33333
position  2:    T:0.22222    C:0.20000    A:0.33333    G:0.24444
position  3:    T:0.26667    C:0.24444    A:0.21111    G:0.27778
Average         T:0.24815    C:0.21481    A:0.25185    G:0.28519

#5: PITG_23267T0   
position  1:    T:0.27381    C:0.19048    A:0.22619    G:0.30952
position  2:    T:0.20238    C:0.23810    A:0.35714    G:0.20238
position  3:    T:0.33333    C:0.15476    A:0.20238    G:0.30952
Average         T:0.26984    C:0.19444    A:0.26190    G:0.27381

#6: PITG_23293T0   
position  1:    T:0.28788    C:0.19697    A:0.21212    G:0.30303
position  2:    T:0.19697    C:0.22727    A:0.36364    G:0.21212
position  3:    T:0.30303    C:0.18182    A:0.21212    G:0.30303
Average         T:0.26263    C:0.20202    A:0.26263    G:0.27273

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      26 | Ser S TCT      19 | Tyr Y TAT      12 | Cys C TGT      19
      TTC      12 |       TCC       5 |       TAC       0 |       TGC      24
Leu L TTA       2 |       TCA      10 | *** * TAA       0 | *** * TGA       0
      TTG       6 |       TCG       4 |       TAG       0 | Trp W TGG       1
------------------------------------------------------------------------------
Leu L CTT       2 | Pro P CCT       6 | His H CAT      10 | Arg R CGT       0
      CTC       0 |       CCC       2 |       CAC       7 |       CGC       4
      CTA       9 |       CCA       7 | Gln Q CAA      19 |       CGA       7
      CTG      27 |       CCG       6 |       CAG      13 |       CGG       9
------------------------------------------------------------------------------
Ile I ATT       7 | Thr T ACT       0 | Asn N AAT      14 | Ser S AGT       5
      ATC       1 |       ACC       8 |       AAC       0 |       AGC       2
      ATA       2 |       ACA       1 | Lys K AAA      15 | Arg R AGA       2
Met M ATG       8 |       ACG      16 |       AAG      33 |       AGG       8
------------------------------------------------------------------------------
Val V GTT      13 | Ala A GCT      11 | Asp D GAT      23 | Gly G GGT       8
      GTC       6 |       GCC       2 |       GAC      21 |       GGC       9
      GTA       3 |       GCA      14 | Glu E GAA      15 |       GGA      16
      GTG       1 |       GCG      11 |       GAG      17 |       GGG      16
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.24306    C:0.22222    A:0.21181    G:0.32292
position  2:    T:0.21701    C:0.21181    A:0.34549    G:0.22569
position  3:    T:0.30382    C:0.17882    A:0.21181    G:0.30556
Average         T:0.25463    C:0.20428    A:0.25637    G:0.28472

Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
  0.01695921  0.00998171  0.01182300  0.01705612
  0.01655219  0.00974215  0.01153924  0.01664678
  0.02699907  0.01589088  0.00000000  0.00000000
  0.01763758  0.01038098  0.00000000  0.01773837
  0.01550557  0.00912613  0.01080960  0.01559417
  0.01513343  0.00890711  0.01055017  0.01521991
  0.02468486  0.01452881  0.01720888  0.02482592
  0.01612579  0.00949118  0.01124198  0.01621794
  0.01477874  0.00869835  0.01030290  0.01486319
  0.01442405  0.00848959  0.01005563  0.01450648
  0.02352776  0.01384777  0.01640221  0.02366221
  0.01536989  0.00904628  0.01071501  0.01545772
  0.02253153  0.01326141  0.01570769  0.02266028
  0.02199077  0.01294314  0.01533071  0.02211643
  0.03587019  0.02111217  0.02500665  0.03607517
  0.02343279  0.01379187  0.01633600  0.02356669



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.)

PITG_23265T0        
PITG_23253T0         0.7388 (0.1143 0.1547)
PITG_23257T0         0.5661 (0.2657 0.4694) 0.5585 (0.2359 0.4223)
PITG_23264T0         0.4754 (0.1086 0.2285) 0.4895 (0.1580 0.3229) 0.5040 (0.1709 0.3391)
PITG_23267T0        -1.0000 (0.0052 0.0000) 0.7996 (0.1242 0.1553) 0.7913 (0.2544 0.3214) 0.4998 (0.1145 0.2291)
PITG_23293T0         0.3307 (0.0214 0.0648) 0.6077 (0.0901 0.1483) 0.5382 (0.1653 0.3071) 0.5146 (0.0663 0.1288) 0.3307 (0.0214 0.0648)


Model 7: beta (10 categories)


TREE #  1:  ((((1, 2), 3), 4), 5, 6);   MP score: -1
check convergence..
lnL(ntime:  9  np: 12):  -1085.258650      +0.000000
   7..8     8..9     9..10   10..1    10..2     9..3     8..4     7..5     7..6  
 0.013157 0.000004 0.000004 0.000004 0.450945 1.280990 0.536965 0.000004 0.122969 1.933218 0.005041 0.005042

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

tree length =   2.40504

((((1: 0.000004, 2: 0.450945): 0.000004, 3: 1.280990): 0.000004, 4: 0.536965): 0.013157, 5: 0.000004, 6: 0.122969);

((((PITG_23265T0: 0.000004, PITG_23253T0: 0.450945): 0.000004, PITG_23257T0: 1.280990): 0.000004, PITG_23264T0: 0.536965): 0.013157, PITG_23267T0: 0.000004, PITG_23293T0: 0.122969);

Detailed output identifying parameters

kappa (ts/tv) =  1.93322

Parameters in M7 (beta):
 p=  0.00504  q=  0.00504


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  1.00000  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

   7..8       0.013    302.2     99.8   0.5000   0.0035   0.0070    1.1    0.7
   8..9       0.000    302.2     99.8   0.5000   0.0000   0.0000    0.0    0.0
   9..10      0.000    302.2     99.8   0.5000   0.0000   0.0000    0.0    0.0
  10..1       0.000    302.2     99.8   0.5000   0.0000   0.0000    0.0    0.0
  10..2       0.451    302.2     99.8   0.5000   0.1204   0.2408   36.4   24.0
   9..3       1.281    302.2     99.8   0.5000   0.3420   0.6841  103.4   68.3
   8..4       0.537    302.2     99.8   0.5000   0.1434   0.2868   43.3   28.6
   7..5       0.000    302.2     99.8   0.5000   0.0000   0.0000    0.0    0.0
   7..6       0.123    302.2     99.8   0.5000   0.0328   0.0657    9.9    6.6


Naive Empirical Bayes (NEB) analysis
Time used:  2:02


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


TREE #  1:  ((((1, 2), 3), 4), 5, 6);   MP score: -1
check convergence..
lnL(ntime:  9  np: 14):  -1073.575282      +0.000000
   7..8     8..9     9..10   10..1    10..2     9..3     8..4     7..5     7..6  
 0.013828 0.000004 0.000004 0.000004 0.603503 2.093442 0.753012 0.000004 0.185207 2.435233 0.886216 0.005000 0.007538 9.541689

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

tree length =   3.64901

((((1: 0.000004, 2: 0.603503): 0.000004, 3: 2.093442): 0.000004, 4: 0.753012): 0.013828, 5: 0.000004, 6: 0.185207);

((((PITG_23265T0: 0.000004, PITG_23253T0: 0.603503): 0.000004, PITG_23257T0: 2.093442): 0.000004, PITG_23264T0: 0.753012): 0.013828, PITG_23267T0: 0.000004, PITG_23293T0: 0.185207);

Detailed output identifying parameters

kappa (ts/tv) =  2.43523

Parameters in M8 (beta&w>1):
  p0=  0.88622  p=  0.00500 q=  0.00754
 (p1=  0.11378) w=  9.54169


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

p:   0.08862  0.08862  0.08862  0.08862  0.08862  0.08862  0.08862  0.08862  0.08862  0.08862  0.11378
w:   0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  1.00000  1.00000  1.00000  1.00000  9.54169

dN & dS for each branch

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

   7..8       0.014    298.1    103.9   1.4402   0.0050   0.0035    1.5    0.4
   8..9       0.000    298.1    103.9   1.4402   0.0000   0.0000    0.0    0.0
   9..10      0.000    298.1    103.9   1.4402   0.0000   0.0000    0.0    0.0
  10..1       0.000    298.1    103.9   1.4402   0.0000   0.0000    0.0    0.0
  10..2       0.604    298.1    103.9   1.4402   0.2184   0.1517   65.1   15.8
   9..3       2.093    298.1    103.9   1.4402   0.7577   0.5261  225.9   54.7
   8..4       0.753    298.1    103.9   1.4402   0.2725   0.1892   81.2   19.7
   7..5       0.000    298.1    103.9   1.4402   0.0000   0.0000    0.0    0.0
   7..6       0.185    298.1    103.9   1.4402   0.0670   0.0465   20.0    4.8


Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: PITG_23265T0)

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

    18 H      0.869         8.422
    78 S      0.974*        9.316
   119 T      0.999**       9.536
   122 *      0.842         8.195
   123 *      0.885         8.558
   125 S      0.988*        9.439
   128 I      0.783         7.684
   129 A      0.611         6.221
   130 R      0.695         6.935
   131 V      0.990**       9.456


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: PITG_23265T0)

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

    17 I      0.672         2.847 +- 1.967
    18 H      0.964*        4.162 +- 1.684
    23 F      0.734         3.145 +- 2.009
    31 V      0.720         3.084 +- 2.016
    33 E      0.598         2.528 +- 1.799
    35 Q      0.717         3.057 +- 2.015
    38 Y      0.736         3.101 +- 1.835
    45 M      0.667         2.730 +- 1.627
    55 G      0.503         2.123 +- 1.635
    72 V      0.845         3.535 +- 1.694
    74 A      0.853         3.585 +- 1.711
    78 S      0.996**       4.292 +- 1.597
   101 D      0.888         3.756 +- 1.701
   108 D      0.686         2.924 +- 1.897
   110 S      0.870         3.649 +- 1.678
   115 S      0.597         2.494 +- 1.729
   117 A      0.626         2.689 +- 1.911
   118 A      0.626         2.689 +- 1.911
   119 T      1.000**       4.306 +- 1.589
   122 *      0.970*        4.178 +- 1.660
   123 *      0.963*        4.161 +- 1.690
   124 Y      0.864         3.641 +- 1.717
   125 S      0.997**       4.295 +- 1.597
   126 F      0.754         3.133 +- 1.721
   127 C      0.931         3.955 +- 1.659
   128 I      0.972*        4.179 +- 1.642
   129 A      0.957*        4.096 +- 1.650
   130 R      0.941         4.049 +- 1.710
   131 V      0.998**       4.298 +- 1.595
   132 R      0.876         3.756 +- 1.803



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  0.017  0.280  0.515  0.185  0.002
p :   0.640  0.273  0.070  0.014  0.002  0.000  0.000  0.000  0.000  0.000
q :   0.010  0.146  0.108  0.102  0.100  0.101  0.103  0.107  0.110  0.114
ws:   0.000  0.149  0.398  0.223  0.104  0.054  0.031  0.019  0.013  0.009

Time used:  5:58

Time used:  5:58
