02_AG Problem (All Positive Indels)

[jpalmer37]

The data can be found here 02_AG Check

MSA = .fasta Variable Seqs = .csv (only the cherry sequences are shown) Tree = .tree

Let me know if you need more files.

[jpalmer37]

Here is the box and whisker plot you requested.

[ArtPoon]

That's interesting, AG is definitely different compared to some of the other groups. What are the units of branch length?

[jpalmer37]

Total elapsed time in years. (years sequence 1 + years sequence 2 = total years of cherry pair)

[ArtPoon]

Years is a difficult scale to compare across subtypes because they will vary in degrees of confidence in calibrating the respective molecular clocks. Can you make the same barplot with branch lengths in expected substitutions, i.e., directly from the ML tree reconstructions prior to clock analysis?

[jpalmer37]

Here's a boxplot of expected substitutions. For the time being, I excluded subtype F1 because it was giving me some trouble with a tip numbering error.

[jpalmer37]

Strangely, subtype F1 appeared to work fine when I plotted the rooted trees here (made via rtt) as opposed to the unrooted trees in my previous comment.