I am dealing with an ITS matrix with a lot of gaps. As there are a lot of potential information, I would like to use these gaps coded as characters. That would help me both to include more of the variation in the analysis and keep some haplotypes that would be exactly the same if the gap information is removed. Is that possible in BPP?
Thanks in advance,
David Ortiz
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You can keep the gaps in the data. They will be treated as question marks.
That is not perfect but is sometimes better than removing all sites with gaps.
Ziheng
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi:
I am dealing with an ITS matrix with a lot of gaps. As there are a lot of potential information, I would like to use these gaps coded as characters. That would help me both to include more of the variation in the analysis and keep some haplotypes that would be exactly the same if the gap information is removed. Is that possible in BPP?
Thanks in advance,
David Ortiz
You can keep the gaps in the data. They will be treated as question marks.
That is not perfect but is sometimes better than removing all sites with gaps.
Ziheng