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Change default input sequence type behavior for MSA

Workum, Dirk-Jan van requested to merge fix_msa_alignment_type into develop

Preparing for the introduction of variation in PanTools (!128 (merged)), we decided to split the default input sequences taken for pantools msa in boolean flags. Therefore, this merge request introduces --align-protein and --align-nucleotide options to pantools msa (as well as MSA depending subcommands: pantools core_phylogeny and pantools consensus_tree).

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