ML no Paup
Preparar um arquivo nexus como feito na prática Parcimonia no PAUP, mas utilizar o seguinte Paup Block, incluindo nele o modelo selecionado para os seus dados pelo JModelTeste.
BEGIN PAUP; exclude constant; set criterion=likelihood; [DEFINICAO DO MODELO EVOLUTIVO] [!Likelihood settings from best-fit model (TPM2uf+I+G) selected by AICc with jModeltest 2.1.10 v20160303 on Wed May 03 06:57:07 PDT 2017] Lset base=(0.3030 0.2143 0.1969 ) nst=6 rmat=(0.7632 4.7474 0.7632 1.0000 4.7474) rates=gamma shape=0.1670 ncat=4 pinvar=0.6030; set autoclose=yes warnreset=no increase=no maxtrees=100000; hsearch addseq=random nreps=1000; savetrees brlens=yes file=myML.trees append=yes; gettrees file=myML.trees; outgroup ac1OUTG1; contree all/ le50 root=outgroup outroot=monophyl replace treefile=myML.tree; gettrees file=myML.tree; savetrees /fmt=altnex brlens=yes file=myMLconsenso.t; END;