Input file MrBayes CO1
#NEXUS
begin mrbayes ;
set autoclose=yes nowarn=yes ;

log start filename=log.txt
exe
Synema_globosum_CO1T3.nex ;

charset CO1_12 = 1-1239\3 2-1239\3;
charset CO1_3   = 3-1239\3;

partition full = 2 : CO1_12, CO1_3 ;
set partition = full ;

lset applyto = (all) nucmodel=4by4 nst=mixed rates=invgamma ;

unlink statefreq =(all) revmat =(all) shape =(all) pinvar=(all)
prset applyto = (all) ratepr=variable ; 

mcmc nruns = 4 ngen=20000000 temp=0.1 nchain=4 samplefreq=1000 ;
mcmc ;

sump burninr=0.5 ;
sumt burinfr=0.5;

log stop;
end;

Input file MrBayes ITS2
#NEXUS

begin mrbayes ;
set autoclose=yes nowarn=yes ;

log start filename=log.txt
exe
Alignment_ITS_Synglob_Cymbacha.nex

charset ITS2 = 1-386

partition full = 1 : ITS2;
set partition = full ;

lset applyto = (all) nucmodel=4by4 nst=mixed rates=invgamma ;

unlink statefreq =(all) revmat =(all) shape =(all) pinvar=(all)
prset applyto = (all) ratepr=variable ; 

mcmc nruns = 4 ngen=20000000 temp=0.1 nchain=4 samplefreq=1000 ;
mcmc ;

sump burninr=0.5 ;
sumt burinfr=0.5;

log stop;
end;

Input files RAxML CO1
raxmlHPC -s Synema_globosum_CO1T3.phy -n CO1_RaxML_plus_outgroup -m GTRCAT -p 2135246 -f a -x 1434897 -N 1000 -q partitionfileCO1_plus.txt

[PartitionfileCO1_lpus.txt]
DNA, CO1_firstSecond = 1-1239\3, 2-1239\3
DNA, CO1_third = 3-1239\3

Input files RAxML ITS2
raxmlHPC -s ITS2_Synglob_Cymbacha.phy -n ITS2_RaxML_plus_outgroup -m GTRCAT -p 2135246 -f a -x 1434897 -N 1000 -q partitionfileITS2.txt