Hi!
I need to know the best evolution models for each partition of a DNA alignment. My nexus file contains an indel coding. PartitionFinder needs a PHYLIP file to run an analysis. However, when I convert my nexus file into a phylip one (through Geneious), the indel coding is not referred. So, PartitionFinder will run without take into account that there is a gap coding...
Have I to use an other software? Or there is a way to implement indel coding in PartitionFinder?
Thanks!
What I did was to launch PartitionFinder on the alignment without the binary sites, which instead were placed in a separate alignment. To set the IQ-TREE partition file, just add the partition for binary sites choosing a binary model.
I leave you one of my partition files with the alignment file and the binary sites file.
Hello Alessandro,
Thank you, but I think I don't understand what you did. How did you get the best model for the indels?
Can you show me your partition_finder.cfg file, please? And, can you tell me which software did you use to code the indels?
To code the indels I used GapCoder, which is not available anymore. But I think there are other programs that do the same work.
To test the partition models you can use PartitionFinderMorphology, however it has only two binary models (BINARY+G and BINARY+G+A) and you can test them only once at a time.
I run both and kept the one with the highest score. I leave you the comand and also a .cfg as example
PartitionFinderMorphology.py partition_finder.cfg --raxml
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