In order to discover the best evolutionary model and partitioning scheme for Bayesian analysis, I am trying to run the command line
iqtree -s aln_seqs.fas -p aln_seqs.nex -m MF+MERGE -mset mrbayes -nt AUTO,
but I get it as answer:
Expecting floating-point number, but found "aln_seqs.nex" instead.
It seems to me that there is a problem with the content of my .nex file, right? Or is the problem with the command line I'm implementing? The contents of this .nex file are
#nexus begin sets; charset cd1 = 2 -. \ 3; charset cd2 = 3 -. \ 3; charset cd3 = 1 -. \ 3; end;
Does anyone imagine what I'm doing wrong? I couldn't find an answer in the documentation.
Thanks a lot!
You might be mixing IQ-TREE manuals with different executable versions. For versions 1.x, -spp would supply the partitions file, whereas for versions 2.x -p does. So, possibly re-install the most recent IQ-TREE version. You also might want "-m MFP+MERGE" ?
That was it, Tyler!!! It worked in both modes: MF + MERGE and MFP + MERGE.
Thank you so much for your help!
All the best!
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