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actually, if the problem is only coming from FastTree, we could also extend the FastTree-Wrapper to include a label transformation on the fly. or are there other places with limits? Mafft?
The enforced length limit on the fasta IDs is annoying.
FastOMA/FastOMA/check_input.py
Line 50 in 38b2991
we could replace all the IDs with a lookup table. however, there are a few things to consider:
One option could be to store the mapping in a sqlite database. comments wellcome.
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