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let core_snp_tree search for alignment with updated msaNames variable instead...

Workum, Dirk-Jan van requested to merge hotfix_core_snp_tree into master

problem: homology groups that could not be trimmed were causing pantools core_snp_tree to crash, since the function was still expecting trimmed output based on hmNodeList

solution: let core_snp_tree search for alignment with the updated msaNames variable instead of the not updated hmNodeList

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