Fixed ignoring untrimmed MSA for core_phylogeny and consensus_tree

In !195 (merged), we made sure that pantools core_phylogeny and pantools consensus_tree don't run MSA under the hood anymore. However, that causes issues when with pantools msa groups could not be trimmed. There is no way of knowing which groups these were for pantools core_phylogeny and pantools consensus_tree. This merge request fixes that by reading the text file that pantools msa creates which contains all homology groups that could not be trimmed ("groups_excluded_based_on_trimming.txt") and excluding them from analysis.