Multiple markers/loci per cluster issue about phylotar HOT 4 OPEN

Hi @Bunholi,

Unfortunately, the corrections did no solve the problem.
I think that it is a software issue.

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Hi,

I've managed to re-run your analysis for Asteracea and I'm looking over the clusters. So that I can repeat your process, how are you determining that there is a mix of ITS and trnL in the first cluster?

The top thing I've noticed is ...

#specify the sequence IDs per cluster
sids <- reduced@clstrs[[i]]@sids

Should be:

#specify the sequence IDs per cluster
sids <- selected@clstrs[[i]]@sids

Where does the "reduced" phylota object originate? Mixing sids across different phylota objects could be causing the mixing of sequences in a cluster.

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Hi @bpjburger did you solve the problem following @DomBennett correction?
I am planning to do the same around here

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For info, we're looking for a new maintainer / a new maintainer team for this package, see #57 and feel free to volunteer, we'd be happy to help.

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