14 June 2023 PAINT Conference Call

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Present

Marc, Dustin, Anushya, Paul T, Huaiyu, Pascale


Agenda

PANTHER 18 build

The node forward tracking from v.15 to v.18 is not better than that from v.15 to 17. After more careful review of trees, the conclusion from the last call that trees map better from 15 to 18 is not true either. It seems that the differences in tree topology were caused by the sequence alignment.

Node forward tracking stats after correcting 15.0 -> 18.0 stats from 2023-05-17 call:

  • 15.0 -> 18.0
    • LEAF - 1766795 / 1968819 = 89.7%
    • SPECIATION - 1018630 / 1138527 = 89.4%
    • DUPLICATION - 280400 / 367319 = 76.3%
    • HORIZONTAL TRANSFER - 4248 / 6838 = 62.1%
    • ALL - 3070073
  • 15.0 -> 17.0
    • LEAF - 1847433 / 1973248 = 93.6%
    • SPECIATION - 1025670 / 1137262 = 90.1%
    • DUPLICATION - 299119 / 371052 = 80.6%
    • HORIZONTAL TRANSFER - 4436 / 6973 = 63.6%
    • ALL - 3176658
  • 17.0 -> 18.0
    • LEAF - 1887652 / 1968819 = 95.8%
    • SPECIATION - 1078875 / 1138527 = 94.7%
    • DUPLICATION - 309757 / 367319 = 84.3%
    • HORIZONTAL TRANSFER - 5374 / 6838 = 78.6%
    • ALL - 3281658

Here is the proposed plan based on these data.

  • Continue to review families in PANTHER17.0.
  • We will test ways to keep the alignment more stable in future PANTHER builds, probably starting in PANTHER19.0.

PAN-GO paper

Status update. What remains to be do? https://docs.google.com/document/d/1UHaO-ti3WN7r4zcbZnyRyMYUEhJh-d5NqljTktzLQyg/edit