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The program run and give me an output p.stats. However, the ancestral sequence for both clade is the same, with posterior probability of 1 for an amino-acid for a given site. The thing which is very strange is the fact that the ancestral sequence corresponds always to the last sequence in my matrice (even if it's the outgroup or not). I already tried to swap individuals, I have always an ancestral sequence corresponding to the last individual sequence.
Thank you for help.
The text was updated successfully, but these errors were encountered:
I try to reconstruct ancestral sequence of protein. I use the parameters under (i cut protein for you to see better) :
begin data;
dimensions ntax=4 nchar=1057;
format datatype=protein missing=? gap=-;
end;
begin mrbayes;
outgroup Trichechus_manatus;
prset aamodelpr=mixed;
constraint Elephantiforme -1 = 1 2 3;
constraint Elephantidae -1 = 1 2;
prset topologypr = constraints(Elephantidae, Elephantiforme);
report ancstates=yes;
mcmc nchains = 4 ngen=30000;
sumt;
sump;
end;
The program run and give me an output p.stats. However, the ancestral sequence for both clade is the same, with posterior probability of 1 for an amino-acid for a given site. The thing which is very strange is the fact that the ancestral sequence corresponds always to the last sequence in my matrice (even if it's the outgroup or not). I already tried to swap individuals, I have always an ancestral sequence corresponding to the last individual sequence.
Thank you for help.
The text was updated successfully, but these errors were encountered: