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TODO.md

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Repository setup

  • Begin USAGE wiki
  • Begin INSTALL wiki
  • Begin Output wiki
  • Begin tool wiki
  • Build pypi package
  • Build conda package
  • Update intro page
  • Add issue format
  • Mirror with GitHub

Algorithm improvements

  • Merge loci extensions that overlap after the second round
  • Option to merge adjacent reported loci that belong to the same HLG on output based on a gene intermediance
  • Fix rooting system for nodes that overlap current root/ambiguous
  • Multiprocess null generation
  • Lineage-based thresholds
  • Standardize code annotation
  • Account for tandem dup HGs
  • Tune hyperparameters for global maximum quality output
    • High percentage of 1 domain/reference cluster
  • Convert sliding window to nucleotide-based slide
  • Account for alternate splicing appropriately (gene-wise v RNA-wise)
  • Implement random sampling probability HGps and HGxs
  • Account for duplicates of HGs on edge of cluster
  • Add Pfam extraction feature
  • Add GO extraction feature
  • Output networks as interactable files
  • Phylogeny-based method of GCL calculation
  • Add a force skip to filtering that reads in old runs and converts
  • Output version in the log, have a version output statement
  • aPDS that removes the signal of HLG loss
  • rPDS calculation with GCL threshold in cloci2stats

Quality of life

  • pruning discrepancies from microsynteny tree and input database and removing from analysis
  • common visualization outputs