Goals

[tiagolbiotech]

Very Short term

Goal	Priority	Difficulty
Update subcluster_dictionary.csv	Very High	Medium
Incorporate subcluster_dictionary.csv search by smCOG	Very High	Medium
Add --database option to avoid downloading same clusters again	Very High	Low
Run multigeneBLAST in parallel	High	High
Add multiple strains option	Very High	Low
Incorporate hits within same genomes	High	Medium
Incorporate calibration curve	Very High	High

Short term

Goal	Priority	Difficulty
Implement "light memory option", deleting unused iterations
Remove multiple self-loops	Medium	Medium
Incorporate pFAM domais and Jaccard index	Very High	Medium
Generate aligment vizualition for gene cluster families	High	High
Automate network plotting	High	Low

Long term

Goal	Priority	Difficulty
Add border refinement option	High	Medium
Add "supercluster" separation option	High	Very High
Improve matrix rules	High	Very High
Improve filtering options	Low	High
Incorporate bidirectional alignment	Low	High
Implement interface	Low	Very High