Open lutteropp opened 5 years ago
Done, but this slightly worsened the RF-distances for some reason.Probably because now we choose smaller kmer sizes?
Normalized RF-distances before the change: g1 V8: 0.5925926 g2 V8: 0.5185185 g3 V8: 0.5555556 m1 V8: 0.0 m2 V8: 0.05882353 m3 V8: 0.05882353 brucella V8: 0.1 roseobacter V8: 0.4482759 w252 V8: 0.125 w2016 V8: 0.0625 bacteria V8: 0.9285714 faba V8: 0.2666667 59 V8: 0.1964286 (edited)
Normalized RF-distances after the change: g1Mat V9: 0.5925926 g2Mat V9: 0.5555556 g3Mat V9: 0.5925926 m1Mat V9: 0.0 m2Mat V9: 0.1176471 m3Mat V9: 0.0 brucellaMat V9: 0.1 ecoliMat V9: 0.3461538 roseobacterMat V9: 0.5517241 w252Mat V9: 0.125 w2016Mat V9: 0.0 bacteriaMat V9: 1.0 fabaMat V9: 0.8 59Mat V9: 0.5357143
Maybe we shouldn't allow for a kmer-size that leads to paralogs in some of the taxa? But then, this would be back to before the change.
Maybe we need something like "We need the kmer size for the kept non-paralog taxa to be at least X larger than the kmer-size for the paralog taxa that were discarded"
Maybe just delete the taxon which has a paralogy issue from the block?