bede / vespasian Goto Github PK

If the site under selection is an ambiguous character i.e. "N" in the species for which CodeML uses to identify the amino acid, CodeML states this as an * character. This causes problems during Vespasian report where no amino acid is given as a site.

CodeML out:

      Pr(w>1)     post mean +- SE for w

   210 -      0.956-        2.375
   263 *      0.614         1.678
   303 A      0.867         2.194
   345 A      0.623         1.696
   455 R      0.589         1.627

Vespasian report:

OG0013728_pruned.aln    m3Discrtk3      10      -4741.630387    p0=0.25134 p1=0.7097 p2=0.03897 w0=0.01497 w1=0.42793 w2=2.46432        no      210-:0.956 2630.614:1.678 303A:0.867 345A:0.623 455R:0.589               codeml/OG0013728_pruned.aln/OG0013728_pruned.aln/m3Discrtk3/Omega10/out

Proceed anyway with non zero exits

Derooting needs rethinking since niemasd/TreeSwift@4ed75ce#diff-60f61ab7a8d1910d86d9fda2261620314edcae5894d5aaa236b821c7256badd7

Pinning to treeswift==1.1.14 for time being

Docker, github actions?

https://packages.ubuntu.com/search?keywords=paml&searchon=names&suite=all&section=all

• Codon alignment
• Automatic terminal stop codon removal / input alignment validation
• ?

Research visualisation possibilities. See ETE3.
HTML output for sites above threshold?