      4   1497

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



Printing out site pattern counts


         4        696  P

Gallus_gallus                   AAA AAC AAC AAC AAC AAC AAC AAC AAG AAG AAG AAG AAG AAG AAT AAT AAT AAT AAT AAT ACA ACA ACA ACC ACC ACC ACC ACC ACC ACC ACC ACG ACG ACG ACG ACG ACT ACT AGA AGA AGA AGC AGC AGC AGC AGG AGG AGT AGT AGT ATA ATA ATA ATA ATA ATA ATC ATC ATC ATC ATC ATC ATC ATC ATG ATG ATG ATG ATT ATT ATT ATT CAA CAA CAA CAC CAC CAG CAG CAG CAG CAG CAT CAT CCA CCA CCC CCC CCC CCG CCT CCT CCT CGA CGC CGG CGG CGG CGT CGT CTA CTA CTA CTA CTC CTC CTC CTC CTC CTC CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTT CTT CTT CTT CTT GAA GAA GAA GAA GAC GAC GAC GAC GAC GAG GAG GAG GAT GAT GCA GCA GCA GCA GCA GCA GCA GCA GCC GCC GCC GCC GCC GCC GCC GCC GCG GCT GCT GCT GCT GCT GCT GCT GGA GGA GGA GGA GGC GGC GGC GGC GGG GGG GGG GGG GGG GGT GGT GGT GGT GGT GTA GTC GTC GTC GTC GTG GTG GTG GTG GTT GTT GTT TAC TAC TAT TAT TAT TAT TCA TCA TCA TCA TCA TCC TCC TCC TCC TCG TCG TCT TCT TGC TGC TGG TGG TGT TTA TTC TTC TTC TTC TTC TTG TTG TTG TTG TTG TTT TTT TTT 
Meleagris_gallopavo             ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... .T. .T. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ..C ... ... ..C ... ... ... ... ... .G. ... ... ... ... ... ..A ... ... ... ... ... ... ... ... T.. T.. ..C ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ..C ... A.. ... ... ... ... ... ... ..G A.. ..A ... ... ... ... ... ... ..A ..A ..C ... ... ... ... ... ... ... ... ..T ... ... ..G ..T ..A ... ... ... ... ..G ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ..G ..A ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... A.. ... ... ... ... ... ... ... 
Taeniopygia_guttata             ... ..A ... ... ..T .G. CG. G.T G.C ..C ... ... .CC C.. ..C ..C ..C ... .GC GC. ... ... ..T ..A ... ... ..G ..T ..T G.. GT. T.A ..C .T. .A. TT. ... ... .A. ... GA. .A. ..A ... GA. .A. ... .A. ..A ... ... ... ... ..T ..T GC. .C. ... ... ..T ..T C.. C.. G.. .A. ... GCA G.. ..A ..C ..C ... A.. ..C .G. ... ..T ..A ..C ... ... .T. ... ... ... ... ..A ..T .G. ..A ..A ..A ... ..C ... ... .A. ... ... ..C ... ..C ..G ..T .G. A.. ... ..T ..T T.T ... ..A ... ... ... ... ..T ..T T.. ... T.A ..C ..G ... T.A T.C ... ..C ..G ..T A.. AG. ... ..T C.. A.A C.T ... ..C ... ..G AAG ... ..G ..T .GT T.G ... A.T T.. ..A ..A ... ..G ..T .T. .G. ..A ... ..A ... ... ... T.. C.. .CT ... ..T ... ..G AAG ... ... A.T ..A ... ..T ... ..A ..C ... ... A.. A.. A.A ... ... A.. .CA ... ... AC. A.A ... ... ..T ..C ..C ... ... G.T GT. ... .T. ..G ... G.. ... ... ..A ... ... ... G.G ... C.. ... ... ..G .AT ... ... ..T ..T AC. C.. ..A ... ..T ..C ... ... 
Anas_platyrhynchos              ... ... ... .T. ..T ... ... ..T .G. ... ..A ... ... ... ..C ... C.C ... ... ..C ... ..G ... ... ... .G. ..A ... ..T ... ... G.. ..T ... .T. ... ..A ... ... ... ... ... ..G ... ... ... ... ... .C. ... ... ..C G.. ... G.. ... ... ... ..G ..T G.T ... C.. ... ... ... ... ... ... ..C ... ... ... ..G ... ... ..T ..C ... ..A ... ... ... T.. ... ..C ..G ... ... ..A ..C ..C ... ..C ... ... .A. ... ..C ..C ... ... ..G ..T .G. ... ... ... ..T ... ... ..A ..A ..C ... T.. ... ..T ... ... T.. ..C ..C ... T.G ..C ... ... ... ... ... ..T ... ... ... ... ... ... ..C ... A.. ... ... ..G ... ..G ..C ... ... ... ... ..G ... ..A ... ... .G. ..G ... ..G ..C ..G ... ... ... ... ... ..T ... ..G ..G ... ... ..T ... ... ... ... ... ..C ..C ... ... A.. ... ... ..T ... ... ..C ... ... ... ... ... ... ..C ... ..C ... ..T ... ... ..G ... ..A ... ..A ... ..A ... ..G ... ... ... ... ... ... ..G ... C.. ... ... ..T A.. ... ..A ... ... ..C ..C ... 

    9    1    6    1    1    1    1    1    1    1    1    7    1    1    2
    2    1    7    1    1    3    3    2    1    3    1    1    1    1    2
    1    1    1    1    1    1    1    2    2    2    1    1    1    2    1
    2    3    1    1    3    2    1    1    1    1    1    1    9    1    2
    1    1    1    3    1   11    1    2    1    1    1    4    1    1    1
    6    1    1    2    1    9    1    3    1    6    1    1    3    1    1
    1    2    6    1    2    1    1    1    1    1    1    1    1    1    1
    1   14    1    1    1    1    1    1    3   17    1    1    1    1    1
    1    2    1    6    1    1    6    1    1    1    1    1    4    2    1
    1    1    8    1    9    1    1    8    1    1    1    1    1    1    1
    1    1    3    1    1    1    1    1    1    1    1    1    6    1    1
    1    4    1    2    1    1    1    1    1    1    4    1    1    1    1
    1    2    1    1    1    9    1    1    1    1    4    2    1    6   11
    2    1    1    1    4    1    1    2    1    1    1    1    1    4    1
    1    2    6    1    8    1   15    1    1    1    1   11    3    1    1
    1    1    4    1    1    1    8

CODONML (in paml version 4.9d, February 2017)  GDPD4_MSA_cds_reordered.fa-gb
Model: several dN/dS ratios for branches for branches, 
Codon frequency model: F3x4
ns =   4  ls = 499

Codon usage in sequences
------------------------------------------------------------------------------------------------------
Phe TTT  10  10  15   9 | Ser TCT   8   8   9   7 | Tyr TAT   7   6   8   6 | Cys TGT   1   0   1   1
    TTC  17  17  14  17 |     TCC   7   6   7   5 |     TAC  13  14  13  15 |     TGC   9  10   8   9
Leu TTA   1   1   4   1 |     TCA   6   6   4   7 | *** TAA   0   0   0   0 | *** TGA   0   0   0   0
    TTG   8   9   7  10 |     TCG   2   3   3   4 |     TAG   0   0   0   0 | Trp TGG  16  16  15  16
------------------------------------------------------------------------------------------------------
Leu CTT  11   9  11   9 | Pro CCT   9   8   9   6 | His CAT   4   4   6   4 | Arg CGT   2   1   1   0
    CTC  19  20  19  26 |     CCC   5   5   0   8 |     CAC   7   7  10   8 |     CGC   2   5   7   6
    CTA   4   5   2   4 |     CCA   7   8  12   7 | Gln CAA   3   3   1   3 |     CGA   1   1   2   0
    CTG  29  26  28  22 |     CCG   1   1   0   1 |     CAG  14  14  12  14 |     CGG   3   2   3   2
------------------------------------------------------------------------------------------------------
Ile ATT   7   7   9   8 | Thr ACT   3   3  10   5 | Asn AAT  14  14   9  12 | Ser AGT   5   5   4   4
    ATC  19  20  14  18 |     ACC  11  12   7   8 |     AAC  12  12  15  12 |     AGC   5   5   5   5
    ATA   7   7   8   4 |     ACA   8  10   7   8 | Lys AAA   9  10  14  10 | Arg AGA   5   5   4   5
Met ATG  15  18  13  18 |     ACG   5   2   2   5 |     AAG  12  11  14  10 |     AGG   5   5   3   7
------------------------------------------------------------------------------------------------------
Val GTT   9   9   6  11 | Ala GCT  12  10  14   8 | Asp GAT  10  10  13  10 | Gly GGT   6   7   7   6
    GTC  12  11  15  11 |     GCC  10   9   6  10 |     GAC   9   9   8   9 |     GGC   5   3   4   5
    GTA   1   1   1   3 |     GCA  15  16  16  12 | Glu GAA   9   9   7   9 |     GGA   7   7   6   6
    GTG   7   7   7   6 |     GCG   1   1   3   7 |     GAG  10  10   9  10 |     GGG   8   9   8  10
------------------------------------------------------------------------------------------------------

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

#1: Gallus_gallus  
position  1:    T:0.21042    C:0.24248    A:0.28457    G:0.26253
position  2:    T:0.35271    C:0.22044    A:0.26653    G:0.16032
position  3:    T:0.23647    C:0.32465    A:0.16633    G:0.27255
Average         T:0.26653    C:0.26253    A:0.23914    G:0.23180

#2: Meleagris_gallopavo
position  1:    T:0.21242    C:0.23848    A:0.29259    G:0.25651
position  2:    T:0.35471    C:0.21643    A:0.26653    G:0.16232
position  3:    T:0.22244    C:0.33066    A:0.17836    G:0.26854
Average         T:0.26319    C:0.26186    A:0.24582    G:0.22912

#3: Taeniopygia_guttata
position  1:    T:0.21643    C:0.24649    A:0.27655    G:0.26052
position  2:    T:0.34669    C:0.21844    A:0.27856    G:0.15631
position  3:    T:0.26453    C:0.30461    A:0.17635    G:0.25451
Average         T:0.27589    C:0.25651    A:0.24382    G:0.22378

#4: Anas_platyrhynchos
position  1:    T:0.21443    C:0.24048    A:0.27856    G:0.26653
position  2:    T:0.35471    C:0.21643    A:0.26453    G:0.16433
position  3:    T:0.21242    C:0.34469    A:0.15832    G:0.28457
Average         T:0.26052    C:0.26720    A:0.23380    G:0.23848

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      44 | Ser S TCT      32 | Tyr Y TAT      27 | Cys C TGT       3
      TTC      65 |       TCC      25 |       TAC      55 |       TGC      36
Leu L TTA       7 |       TCA      23 | *** * TAA       0 | *** * TGA       0
      TTG      34 |       TCG      12 |       TAG       0 | Trp W TGG      63
------------------------------------------------------------------------------
Leu L CTT      40 | Pro P CCT      32 | His H CAT      18 | Arg R CGT       4
      CTC      84 |       CCC      18 |       CAC      32 |       CGC      20
      CTA      15 |       CCA      34 | Gln Q CAA      10 |       CGA       4
      CTG     105 |       CCG       3 |       CAG      54 |       CGG      10
------------------------------------------------------------------------------
Ile I ATT      31 | Thr T ACT      21 | Asn N AAT      49 | Ser S AGT      18
      ATC      71 |       ACC      38 |       AAC      51 |       AGC      20
      ATA      26 |       ACA      33 | Lys K AAA      43 | Arg R AGA      19
Met M ATG      64 |       ACG      14 |       AAG      47 |       AGG      20
------------------------------------------------------------------------------
Val V GTT      35 | Ala A GCT      44 | Asp D GAT      43 | Gly G GGT      26
      GTC      49 |       GCC      35 |       GAC      35 |       GGC      17
      GTA       6 |       GCA      59 | Glu E GAA      34 |       GGA      26
      GTG      27 |       GCG      12 |       GAG      39 |       GGG      35
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.21343    C:0.24198    A:0.28307    G:0.26152
position  2:    T:0.35220    C:0.21794    A:0.26904    G:0.16082
position  3:    T:0.23397    C:0.32615    A:0.16984    G:0.27004
Average         T:0.26653    C:0.26202    A:0.24065    G:0.23079

Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
  0.01815163  0.02530345  0.01317645  0.02095017
  0.01123180  0.01565718  0.00815328  0.01296347
  0.01386547  0.01932852  0.00000000  0.00000000
  0.00828830  0.01155392  0.00000000  0.00956615
  0.02058037  0.02868912  0.01493950  0.02375336
  0.01273465  0.01775216  0.00924421  0.01469802
  0.01572071  0.02191473  0.01141182  0.01814446
  0.00939729  0.01309987  0.00682159  0.01084613
  0.02407434  0.03355974  0.01747581  0.02778602
  0.01489664  0.02076598  0.01081362  0.01719334
  0.01838965  0.02563525  0.01334923  0.02122488
  0.01099269  0.01532386  0.00797971  0.01268750
  0.02224214  0.03100563  0.01614579  0.02567133
  0.01376291  0.01918556  0.00999064  0.01588482
  0.01699008  0.02368425  0.01233327  0.01960954
  0.01015608  0.01415762  0.00737240  0.01172190



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

Gallus_gallus       
Meleagris_gallopavo  0.0798 (0.0062 0.0771)
Taeniopygia_guttata  0.2859 (0.0997 0.3489) 0.2574 (0.0949 0.3686)
Anas_platyrhynchos   0.0762 (0.0204 0.2681) 0.0599 (0.0177 0.2950) 0.3211 (0.1027 0.3199)


TREE #  1:  ((1, 2), 3, 4);   MP score: 251
lnL(ntime:  5  np:  8):  -3280.909783      +0.000000
   5..6     6..1     6..2     5..3     5..4  
 0.100795 0.033826 0.036298 0.368226 0.117741 2.736106 0.078994 0.536537

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

tree length =   0.65689

((1: 0.033826, 2: 0.036298): 0.100795, 3: 0.368226, 4: 0.117741);

((Gallus_gallus: 0.033826, Meleagris_gallopavo: 0.036298): 0.100795, Taeniopygia_guttata: 0.368226, Anas_platyrhynchos: 0.117741);

Detailed output identifying parameters

kappa (ts/tv) =  2.73611

w (dN/dS) for branches:  0.07899 0.53654

dN & dS for each branch

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

   5..6      0.101  1085.4   411.6  0.0790  0.0080  0.1011   8.7  41.6
   6..1      0.034  1085.4   411.6  0.0790  0.0027  0.0339   2.9  14.0
   6..2      0.036  1085.4   411.6  0.0790  0.0029  0.0364   3.1  15.0
   5..3      0.368  1085.4   411.6  0.5365  0.0992  0.1849 107.7  76.1
   5..4      0.118  1085.4   411.6  0.0790  0.0093  0.1181  10.1  48.6

tree length for dN:       0.1221
tree length for dS:       0.4745

dS tree:
((Gallus_gallus: 0.033942, Meleagris_gallopavo: 0.036421): 0.101138, Taeniopygia_guttata: 0.184865, Anas_platyrhynchos: 0.118142);
dN tree:
((Gallus_gallus: 0.002681, Meleagris_gallopavo: 0.002877): 0.007989, Taeniopygia_guttata: 0.099187, Anas_platyrhynchos: 0.009333);

w ratios as labels for TreeView:
((Gallus_gallus #0.0789944 , Meleagris_gallopavo #0.0789944 ) #0.0789944 , Taeniopygia_guttata #0.536537 , Anas_platyrhynchos #0.0789944 );


Time used:  0:02
