Use CMAPLE in weekly-tree pipeline, not raxml + garli #1
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These are changes from /home/slj38/ae which had not been committed to skepner/ae. I'm committing them, then making the changes necessary to use cmaple on top
Use CMAPLE for initial tree, not raxml
SamT123
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previously: first ancestor of sequence X with occurence of mutation Y. But this had the problem of the trim being bad if that one sequence is placed outside of the clade we are aiming for (well, it fails because the trimmed tree contains too few sequences) Now: find all nodes with occurrence of mutations, which do have mutations in 'required_mutations' and do not have mutations in 'forbidden mutations. Then check there is only one such clade with > min_tips descendants, and trim to that clade.
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There are enough sequences now that raxml and/or garli fail (I haven't tried myself, this information from Sarah & Poppy). These changes modify the pipeline to use CMAPLE (https://academic.oup.com/mbe/article/41/7/msae134/7700168), a fast recent program which can handle many (>1 million) sequences.
Two other changes: (1) increasing recursion limit in newick.cc to handle larger trees, and (2) committing some changes which were in Sarah's /home/slj38/ae directory.