Produce new cladiifications HMMER models and setup directories

[pcm32]

• Took 0.5 days to delve into code

• Realised that we cannot use a single newick file with complete cladification, but either a separate newick per clade or a fasta identifier to clade assignment, compatible with IDs used in annotation file.

• Go into code and check what is needed, fix some bugs found (0.25)

• Document what is needed (including got refactoring part Python refactoring to new annotation scheme #4 ) (0.15)

• Discuss needs with Eric (0.1)

• Inspect new fasta to clade assignment file given by Eric (1 including fixes)

  • Fix errors

• Try setup scripts with new input from Eric and document process (0.5)

• Finish documentation for setup.