TODO checklist

[iferres]

My TODO checklist

• Add more parameters to control phylogenetic inference step. branch develop
• Add more methods.
• Change from super-gene phylogenetic inference to consensus from many alignments.
• Apply "phylogenetic" algorithm to select between paralogues.
• Add option or create new branch to take into account gene length when merging into orthologous groups. This will be useful to create cgMLST schemes.