I got the wrapper working and I got the result file:
Code:Process this file:
______________READ THE FOLLOWING DATA______________
58 species:{BACI,BALH,BC,BCAH1_,BCAH8_,BCB4_,BCE,BCZK,BT,G924_,GBAA_,bce10_,bce11_,bce12_,bce13_,bce14_,bce15_,bce16_,bce17_,bce18_,bce19_,bce1_,bce20_,bce21_,bce22_,bce23_,bce25_,bce26_,bce27_,bce28_,bce29_,bce2_,bce30_,bce4_,bce5_,bce6_,bce7_,bce98_,bce9_,bceKB_,bmyc1_,bmyc2_,bmyc3_,bpmyx,bth10_,bth11_,bth12_,bth13_,bth14_,bth1_,bth2_,bth3_,bth4_,bth5_,bth6_,bth7_,bth8_,bth9_};
Total Sites:984;
Distinct Sites:304
Please enter a 6 character model designation (e.g:010010 defines HKY85):
______________RESULTS______________
Log Likelihood = -12072.9379512379;
Shared Parameters:
GT=0.541603
CT=1.01131
CG=0.315775
AT=0.285311
AC=0.476575
Tree givenTree=((((bce22_:0.0976799,((bmyc2_:0,bmyc3_:0)Node7:0,bpmyx:0.0032812)Node6:0.0643221)Node4:0.0238212,bce98_:0.131946)Node3:0.216181,((((bce14_:0.00101548,bceKB_:0.00219835)Node15:0.0172679,(bce7_:0.0156655,bmyc1_:0.294627)Node18:0.0214159)Node14:0.0131025,bce26_:0.0171199)Node13:0.00101741,(bce29_:0,bce30_:0)Node22:0.0379876)Node12:0.00883453)Node2:0.00195322,((bce17_:0,bce20_:0)Node26:0.00309761,bce19_:0.00346193)Node25:0.0325879,((bce9_:0.296845,((bce28_:0.288973,bce6_:0.020992)Node34:0,(((((BCAH1_:0,bce13_:0)Node41:0.297827,bce1_:0.00227104)Node40:0,BCE:0.00343703)Node39:0,((bce10_:0.00113824,bth1_:0.00113733)Node47:0,G924_:0.00214067)Node46:0)Node38:0.280163,(BCZK:0,(((((((((BCAH8_:0.317937,bce16_:0)Node61:0,bth10_:0.00111754)Node60:0.0595776,bth7_:0)Node59:0,GBAA_:0.289237)Node58:0,bth12_:0.00110489)Node57:0,bth9_:0.28566)Node56:0,BT:0.00110196)Node55:0,BACI:0.286604)Node54:0.00221898,((BALH:0,bce4_:0)Node72:0,bce21_:0.00110873)Node71:0)Node53:0.00222426)Node51:0.0139253)Node37:0.0140406)Node33:0)Node31:0.00544632,((((((((BC:0,bce15_:0)Node83:0.0483543,bce12_:0.0011444)Node82:0,(bce18_:0.00113288,bce27_:0.0496362)Node87:0)Node81:0.195484,bth5_:0.0924736)Node80:0,(BCB4_:0.0010064,bce11_:0)Node91:0.101749)Node79:0.191855,((((bce23_:0.0735883,bce25_:0)Node97:0,bth6_:0.00219817)Node96:0.00220004,bce5_:0.0719465)Node95:0.00101108,bce2_:0)Node94:0)Node78:0.00379512,bth11_:0.00285239)Node77:0.0187235,((bth13_:0.296283,(bth14_:0,bth4_:0.0126539)Node107:0.0145902)Node105:0.00579535,((bth2_:0,bth8_:0)Node111:0,bth3_:0)Node110:0.0336835)Node104:0.00337846)Node76:0.0139159)Node30:0.00457504);
Leaf branches:
bce22_ : 0
bmyc2_ : 0
bmyc3_ : 0
bpmyx : 0
bce98_ : 0
bce14_ : 0
bceKB_ : 0
bce7_ : 0
bmyc1_ : 0
bce26_ : 0
bce29_ : 0
bce30_ : 0
bce17_ : 0
bce20_ : 0
bce19_ : 0
bce9_ : 0
bce28_ : 0
bce6_ : 0
BCAH1_ : 0
bce13_ : 0
bce1_ : 0
BCE : 0
bce10_ : 0
bth1_ : 0
G924_ : 0
BCZK : 0
BCAH8_ : 0
bce16_ : 0
bth10_ : 0
bth7_ : 0
GBAA_ : 0
bth12_ : 0
bth9_ : 0
BT : 0
BACI : 0
BALH : 0
bce4_ : 0
bce21_ : 0
BC : 0
bce15_ : 0
bce12_ : 0
bce18_ : 0
bce27_ : 0
bth5_ : 0
BCB4_ : 0
bce11_ : 0
bce23_ : 0
bce25_ : 0
bth6_ : 0
bce5_ : 0
bce2_ : 0
bth11_ : 0
bth13_ : 0
bth14_ : 0
bth4_ : 0
bth2_ : 0
bth8_ : 0
bth3_ : 0
Internal Branches:
Node7 : 0
Node6 : 0
Node4 : 0
Node3 : 0
Node15 : 0
Node18 : 0
Node14 : 0
Node13 : 0
Node22 : 0
Node12 : 0
Node2 : 0
Node26 : 0
Node25 : 0
Node34 : 0
Node41 : 0
Node40 : 0
Node39 : 0
Node47 : 0
Node46 : 0
Node38 : 0
Node61 : 0
Node60 : 0
Node59 : 0
Node58 : 0
Node57 : 0
Node56 : 0
Node55 : 0
Node54 : 0
Node72 : 0
Node71 : 0
Node53 : 0
Node51 : 0
Node37 : 0
Node33 : 0
Node31 : 0
Node83 : 0
Node82 : 0
Node87 : 0
Node81 : 0
Node80 : 0
Node91 : 0
Node79 : 0
Node97 : 0
Node96 : 0
Node95 : 0
Node94 : 0
Node78 : 0
Node77 : 0
Node107: 0
Node105: 0
Node111: 0
Node110: 0
Node104: 0
Node76 : 0
Node30 : 0
E[Syn subs/nucleotide site] tree:
((((bce22_:0.0742224,((bmyc2_:0,bmyc3_:0):0,bpmyx:0.00227493):0.0607191):0.0097918,bce98_:0.108035):0.159719,((((bce14_:0,bceKB_:0.00219835):0.0131878,(bce7_:0.0126398,bmyc1_:0.215356):0.0151017):0.0110628,bce26_:0.0171199):0,(bce29_:0,bce30_:0):0.0276719):0.00781854):0.00195322,((bce17_:0,bce20_:0):0.00208478,bce19_:0.00346193):0.0244208,((bce9_:0.221631,((bce28_:0.212442,bce6_:0.0179442):0,(((((BCAH1_:0,bce13_:0):0.222642,bce1_:0.00227104):0,BCE:0.00343703):0,((bce10_:0.00113824,bth1_:0.00113733):0,G924_:0.00113341):0):0.206168,(BCZK:0,(((((((((BCAH8_:0.237812,bce16_:0):0,bth10_:0.00111754):0.0482675,bth7_:0):0,GBAA_:0.211175):0,bth12_:0.00110489):0,bth9_:0.208783):0,BT:0.00110196):0,BACI:0.21152):0.00221898,((BALH:0,bce4_:0):0,bce21_:0.00110873):0):0.00222426):0.0129056):0.0140406):0):0.004428,((((((((BC:0,bce15_:0):0.0391534,bce12_:0.0011444):0,(bce18_:0.00113288,bce27_:0.0404362):0):0.195484,bth5_:0.00681538):0,(BCB4_:0,bce11_:0):0.0232256):0.191855,((((bce23_:0.064369,bce25_:0):0,bth6_:0.00219817):0.00220004,bce5_:0.0627291):0,bce2_:0):0):0.00379512,bth11_:0.00285239):0.0156825,((bth13_:0.221967,(bth14_:0,bth4_:0.00447804):0.0123304):0.000924139,((bth2_:0,bth8_:0):0,bth3_:0):0.0275685):0.00337846):0.0139159):0.00457504)
E[Non-syn subs/nucleotide site] tree:
((((bce22_:0.0234575,((bmyc2_:0,bmyc3_:0):0,bpmyx:0.00100627):0.00360306):0.0140294,bce98_:0.0239114):0.0564612,((((bce14_:0.00101548,bceKB_:0):0.00408006,(bce7_:0.00302561,bmyc1_:0.0792714):0.00631422):0.00203966,bce26_:0):0.00101741,(bce29_:0,bce30_:0):0.0103157):0.00101599):0,((bce17_:0,bce20_:0):0.00101283,bce19_:0):0.00816713,((bce9_:0.0752134,((bce28_:0.0765304,bce6_:0.00304787):0,(((((BCAH1_:0,bce13_:0):0.0751849,bce1_:0):0,BCE:0):0,((bce10_:0,bth1_:0):0,G924_:0.00100726):0):0.0739955,(BCZK:0,(((((((((BCAH8_:0.0801247,bce16_:0):0,bth10_:0):0.0113101,bth7_:0):0,GBAA_:0.0780614):0,bth12_:0):0,bth9_:0.0768777):0,BT:0):0,BACI:0.0750832):0,((BALH:0,bce4_:0):0,bce21_:0):0):0):0.00101972):0):0):0.00101831,((((((((BC:0,bce15_:0):0.00920091,bce12_:0):0,(bce18_:0,bce27_:0.00920002):0):0,bth5_:0.0856582):0,(BCB4_:0.0010064,bce11_:0):0.0785229):0,((((bce23_:0.00921931,bce25_:0):0,bth6_:0):0,bce5_:0.00921738):0.00101108,bce2_:0):0):0,bth11_:0):0.00304104,((bth13_:0.0743164,(bth14_:0,bth4_:0.00817586):0.00225975):0.00487121,((bth2_:0,bth8_:0):0,bth3_:0):0.00611502):0):0):0)
Check messages.log details of this run.
I think now it is working.
But I would like to have some help in interpreting the dN/dS
to get the dN/dS for each branch do I need to take value from E[Non-syn subs/nucleotide site] tree: and E[Syn subs/nucleotide site] tree: from each branch and take the ratio?
for example: for the branch bce22_, dN/dS =0.0234575/0.0742224 = 0.3159
Is that right?