I would like to see absolute time just for my own satisfaction as my sequence length is 278 with 274 patterns most of informative.
I looked at my prior for Yule tree which I set upper limit to 13 following discussion suggestions here. Then on clock rate on ucld mean I set it to 1.7e-7 from clock rate of 16s RNA published on frog literature. I have several genera but not many 10 in group 8 out-groups represented by many species close to 1363 with several frog out groups. I am worried about my branch lengths affecting topology although I agreed with most taxa. My mcmc is too long 500000000 with 50000 sampling frequency using my personal 8 thread/core HP envy 2012.
Repeating this would take me another 10 days, anyway, the point is if I want to do it again should I set it to what number? I mean how do I input or incorporate this fixed clock rate? I suppose I learned this value now stands for year or generation? (the one rate I indicated above). Also important is since I discovered that even out-groups are now nested inside the in-group and
root is not on out groups and after checking alignment it seems the sequences imputed after trimming using BMGE on NGfrphylogeny website, the gene portion or sequences may be highly conserved hence even though the genera are diverse this short segment possibly be assumed under strict clock and relaxed may not be appropriate?
So if I decide to rerun it,
1. set clock to strict
2. uniform from 0 to 13?
3. clock rate ucld to ? based on above fixed value?
I appreciate your help!
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