Hi!

I'm working on a phylogenetic inference (molecular) with 205 taxa and 5350 characters (7 different genes).

I've ever made a phylogeny thanks to a supermatrix. There were some polytomies. The problem is that some have lacks of sequences. Thus, I'd like to make a supertree to compare and see if there will be polytomies again or not.

This way, I inferred trees for each genes in ML with IQtree2. Then, I used Clann to make a matrix as a MRP (Matrix Representation with Parsimony) with 7 source trees. Next, I used PAUP to start a heuristic search (in parsimony) with these command lines in my nexus file (as Clann suggested) :

begin paup;

set increase=auto notifybeep=no errorbeep=no;

hs nreps=10 swap=tbr addseq=random;

showtrees;

savetrees FILE=MRP.tree Format=nexus treeWts=yes Append=no replace=yes;

quit;

end;

However, the search is working for hours (since 8:00 pm, yesterday) and it doesn't stop. More than 10 billion rearrangement were tried 1 721 900 trees are already saved, whereas it's only the first replicate. The analysis tells that the best tree is the tree n°3088, but the heuristic search continues.

Regarding the number of taxa and characters, is it normal that it take so much time?

Is there an error in my command lines?

It is the first time I try to build a supertree.

Can you help me?