Arshia shafagh
Hi,
I do not know how can I present a text file, including partitioning by genes and codons. I tried with a text file resemble which I had used for RaxML, bur I have received an error message.
Therefore, I would like to ask you, if possible, could you please tell me how to cope with this issue? Indeed, how can I write my text file for partitioning by genes and codons?
Thanks in advance.
Arshia
Philip Siby
Hi Arshia,
Please read the section of the iqtree documentation (advanced tutorials) http://www.iqtree.org/doc/Advanced-Tutorial#choosing-the-right-partitioning-scheme
Please copy paste the Nexus syntax that you see there and then make necessary changes according to your partition.
Raxml partitioning scheme is also described there.
In the charpartition section please make sure that your partition is just prefixed with a : (colon). And no model name while you are attempting model selection.
#nexus
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.
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charpartition mine = :part1, :part2, :part3, :part4, :part5;
end;
After model selection you will get a best partition (text) file, which can be used for the later tree searches.
Hope I am right (I think I have asked a similar question in this forum few years back... When I was all lost attempting iqtree..),
Other users and the developers will have better insight.
Siby.
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