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Substitution models in mrbayes

##GTR lset applyto=() nst=6 # GTR lset applyto=() nst=6 rates=propinv # GTR + I lset applyto=() nst=6 rates=gamma # GTR + gamma lset applyto=() nst=6 rates=invgamma # GTR + I + gamma

##SYM

lset applyto=() nst=6                           # SYM
prset applyto=() statefreqpr=fixed(equal)

lset applyto=() nst=6 rates=propinv             # SYM + I
prset applyto=() statefreqpr=fixed(equal)

lset applyto=() nst=6 rates=gamma               # SYM + gamma
prset applyto=() statefreqpr=fixed(equal)

lset applyto=() nst=6 rates=invgamma            # SYM + I + gamma
prset applyto=() statefreqpr=fixed(equal)

##HKY

lset applyto=() nst=2                           # HKY
lset applyto=() nst=2 rates=propinv             # HKY + I
lset applyto=() nst=2 rates=gamma               # HKY + gamma
lset applyto=() nst=2 rates=invgamma            # HKY + I + gamma

##K2P

lset applyto=() nst=2                           # K2P
prset applyto=() statefreqpr=fixed(equal)

lset applyto=() nst=2 rates=propinv             # K2P + I
prset applyto=() statefreqpr=fixed(equal)

lset applyto=() nst=2 rates=gamma               # K2P + gamma
prset applyto=() statefreqpr=fixed(equal)

lset applyto=() nst=2 rates=invgamma            # K2P + I + gamma
prset applyto=() statefreqpr=fixed(equal)

##F81

lset applyto=() nst=1                           # F81
lset applyto=() nst=1 rates=propinv             # F81 + I
lset applyto=() nst=1 rates=gamma               # F81 + gamma
lset applyto=() nst=1 rates=invgamma            # F81 + I + gamma

Jukes Cantor

lset applyto=() nst=1                           # JC
prset applyto=() statefreqpr=fixed(equal)

lset applyto=() nst=1 rates=propinv             # JC + I
prset applyto=() statefreqpr=fixed(equal)

lset applyto=() nst=1 rates=gamma               # JC + gamma
prset applyto=() statefreqpr=fixed(equal)

lset applyto=() nst=1 rates=incgamma            # JC + I + gamma
prset applyto=() statefreqpr=fixed(equal)
@oleon12

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oleon12 commented May 15, 2015

Excellent !! This is so usefull, thank you !!

@weatherwatcher42

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weatherwatcher42 commented May 27, 2015

Is it possible to make the TIM2, TIM3 and TIM3ef models in MrBayes 3? I keep getting them as my lowest AICc score but can't figure out how to implement them.
Here's a reference list with more info about the TIM models and others:
http://www.molecularevolution.org/molevolfiles/models/submodels_final.pdf

@Shooroosh

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Shooroosh commented Jun 21, 2016

Thanks

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