Comandos Paup

BEGIN PAUP; Lset base=(0.2267 0.2460 0.3121 ) nst=6 rmat=(0.7890 2.0871 1.3139 0.4863 2.9737)
rates=gamma shape=0.6020 ncat=4 pinvar=0.3200;

BEGIN PAUP Lset base=(0.3098 0.2090 0.0998 ) nst=2 tratio=3.0173 rates=gamma shape=0.2070 ncat=4
pinvar=0;

attach the next block of commands after the data in your PAUP file:

[!Likelihood settings from best-fit model (HKY+G) selected by BIC with jModeltest 2.1.3 on Mon Jul 31 10:29:21
COT 2017]

Outgroup outgroup;
set criterion = parsimony;
hsearch;
describetrees;
savetree root = yes Brlens = yes file = parsimonia;
bootstrap search = heuristic Nreps = 1000;
savetrees from=1 to=1 file = bootstrap_MP format = altnex brlens = yes savebootp = NodeLabels MaxDecimals
= 0;
describetrees;
set criterion = like autoclose = yes root = outgroup storebrlens=yes increase=auto;
log file= Alex.log;
hsearch addseq=random nreps=10 swap=tbr;
savetrees file = maxima_verosimilitud format = altnex brlens = yes maxdecimals = 6;
describetrees;
bootstrap nreps = 10 search = heuristic/ addseq=random swap=tbr hold=1;
savetrees from=1 to=1 file = bootstrap_ML format = altnex brlens = yes savebootp = NodeLabels MaxDecimals =
0;
describetrees;
end;

Comandos mrbayes

begin MRBAYES;
set autoclose=yes nowarnings=no ;
lset nst=6 rates=invgamma ngammacat=4 ;
outgroup halopenitus;
set autoclose=yes;
set nowarnings=yes;
prset shapepr=uniform(0.0001,20.0) ;
prset brlenspr=unconstrained:exponential(10.0) ;
mcmc ngen=2000000 nruns=2 printfreq=100 samplefreq=100 nchains=4 Temp=0.10 savebrlens=yes;
end;

Escribir

sumt filename=YOUR_filename_here.nexus Nruns=2 burnin=10001 contype=Halfcompat;

sump filename=YOUR_filename_here.nex Nruns=2 burnin=10001 Printtofile=YES Outputname=

YOUR_filename_here.nex.p.stat;