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Reorganise all MSA functionalities in a novel class

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

The things changed by this merge request:

  • create novel MultiSequenceAlignment class
  • move all MSA functionalities from pangenome.Classification to pangenome.MultiSequenceAlignment
  • remove large parts of redundancy between pantools msa_of_groups, pantools msa_of_multiple_groups and pantools msa_of_regions, since they only differ in input files
  • let pantools consensus_tree and pantools core_snp_tree use the novel MSA class (since they also had their own MSA code that was largely copied...)
  • add novel MSA functionality for aligning sequences based on containing a specific function
  • make one MSA function that can be used as: pantools msa
  • update help for integration of all MSA functionalities, can be checked by: pantools msa -h

Other changes:

  • remove build.xml file (belonged to Ant, but we are using Maven now)
  • some spelling mistakes
  • removed large amounts of pangenome.Classification that are unused

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