MrBayes で使用するNEXUS 形式は独特であるが、そのためModeltest-NG からスクリプトで変換することができる。Enter the Fungi はそのスクリプトを作成したが使い方を忘れてしまった。使い方を思い出すまで、備忘録としてMrBayes Block を手書きするためのメモを残す。
多遺伝子解析のMrBayes ブロック
#NEXUS
Begin Data;
Dimensions NTax=[タクサ数] NChar=[総塩基数];
Format DataType=DNA Gap=- Missing=?;
Matrix
//PAUP やMEGA で変換したラベル＋配列
;
End;
Begin MrBayes;
CharSet SSU=1-X;
CharSet ITScut=X+1-Y;
Partition Separate=[領域数]:SSU,ITScut;
Set Partition=Sepearate;
Unlink TRatio=(all) RevMat=(all) StateFreq=(all) Shape=(all) PInvar=(all) Correlation=(all);
PrSet ApplyTo=(all) RatePr=Variable;
[SSU]
[ K80_Gamma 1.72270e+004 ] LSet ApplyTo=(1) NucModel=4by4 Nst=2 Rates=Gamma NGammaCat=8; PrSet ApplyTo=(1) StateFreqPr=Fixed(Equal);
[ITScut]
[ GTR_Gamma 6.97411e+004 ] LSet ApplyTo=(2) NucModel=4by4 Nst=6 Rates=Gamma NGammaCat=8; PrSet ApplyTo=(2) StateFreqPr=Dirichlet(1,1,1,1);
End;
領域についてはこちらを参照
@ は領域の番号
"GTR": "lset applyto=(@) nst=6 rates=equal; prset applyto=(@) statefreqpr=dirichlet(1,1,1,1);",
"GTR+I": "lset applyto=(@) nst=6 rates=propinv; prset applyto=(@) statefreqpr=dirichlet(1,1,1,1);",
"GTR+G4": "lset applyto=(@) nst=6 rates=gamma ngammacat=4; prset applyto=(@) statefreqpr=dirichlet(1,1,1,1);",
"GTR+I+G4": "lset applyto=(@) nst=6 rates=invgamma ngammacat=4; prset applyto=(@) statefreqpr=dirichlet(1,1,1,1);",
"SYM": "lset applyto=(@) nst=6 ngammacat=4; prset applyto=(@) statefreqpr=fixed(equal);",
"SYM+I": "lset applyto=(@) nst=6 rates=propinv; prset applyto=(@) statefreqpr=fixed(equal);",
"SYM+G4": "lset applyto=(@) nst=6 rates=gamma ngammacat=4; prset applyto=(@) statefreqpr=fixed(equal);",
"SYM+I+G4": "lset applyto=(@) nst=6 rates=invgamma prset applyto=(@) statefreqpr=fixed(equal);",
"HKY": "lset applyto=(@) nst=2 rates=equal; prset applyto=(@) statefreqpr=dirichlet(1,1,1,1);",
"HKY+I": "lset applyto=(@) nst=2 rates=propinv; prset applyto=(@) statefreqpr=dirichlet(1,1,1,1);",
"HKY+G4": "lset applyto=(@) nst=2 rates=gamma; prset applyto=(@) statefreqpr=dirichlet(1,1,1,1);",
"HKY+I+G4": "lset applyto=(@) nst=2 rates=invgamma; prset applyto=(@) statefreqpr=dirichlet(1,1,1,1);",
"K80": "lset applyto=(@) nst=2 prset applyto=(@) statefreqpr=fixed(equal);",
"K80+I": "lset applyto=(@) nst=2 rates=propinv; prset applyto=(@) statefreqpr=fixed(equal);",
"K80+G4": "lset applyto=(@) nst=2 rates=gamma ngammacat=4; prset applyto=(@) statefreqpr=fixed(equal);",
"K80+I+G4": "lset applyto=(@) nst=2 rates=invgamma ngammacat=4; prset applyto=(@) statefreqpr=fixed(equal);",
"F81": "lset applyto=(@) nst=1 rates=equal; prset applyto=(@) statefreqpr=dirichlet(1,1,1,1);",
"F81+I": "lset applyto=(@) nst=1 rates=propinv; prset applyto=(@) statefreqpr=dirichlet(1,1,1,1);",
"F81+G4": "lset applyto=(@) nst=1 rates=gamma ngammacat=4; prset applyto=(@) statefreqpr=dirichlet(1,1,1,1);",
"F81+I+G4": "lset applyto=(@) nst=1 rates=invgamma ngammacat=4; prset applyto=(@) statefreqpr=dirichlet(1,1,1,1);",
"JC": "lset applyto=(@) nst=1 rates=equal; prset applyto=(@) statefreqpr=fixed(equal);",
"JC+I": "lset applyto=(@) nst=1 rates=propinv; prset applyto=(@) statefreqpr=fixed(equal);",
"JC+G4": "lset applyto=(@) nst=1 rates=gamma ngammacat=4; prset applyto=(@) statefreqpr=fixed(equal);",
"JC+I+G4": "lset applyto=(@) nst=1 rates=incgamma ngammacat=4; prset applyto=(@) statefreqpr=fixed(equal);"