Thanks, Art! I'm still trying to learn the HyPhy batch language (and some of the techniques in this area) and really appreciate your help.
On dNdSRateAnalysis.bf:
- Though dNdSRateAnalysis.bf compares AIC for different models of nonsyn and syn substitution rates, I still had to choose between MG94xREV v. MG94 v. MG94xHKY85, etc. I could/should have used CodonModelCompare.bf to choose the best instantaneous rate matrix model for the dNdSRateAnalysis.bf, right? (In other words, dNdSRateAnalysis.bf does not consider the appropriateness of my rate matrix.)
- To obtain bootstraps and variance for dN and dS values on branches, one uses bootstrap.bf?
- I also wanted to check that it is tractable to create a partition and recalculate dN/dS for every branch with respect to that partition.
On dNdSBivariateRateAnalysis.bf:
- It seems to me that the last two models ("Dual" and "Lineage Dual") of dNdSRateAnalysis are similar, if not identical, to the bivariate rate analyses described in Kosakovsky Pond & Muse (2005) MBE 22(12):2375. It's confusing that there's a separate batch file for the bivariate analyses. Does dNdSBivariateRateAnalysis.bf do anything different from the last two models of dNdSRateAnalysis? Does the bivariate version automatically use discrete distributions instead of gamma distributions? I don't recall being prompted to choose which to use.
dNdSpost.bf was referenced here: Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
My goal is to compare dN/dS rates across the branches of a tree, comparing results from partitioned and nonpartitioned datasets. I hope to do this with the bivariate analyses and bootstrap the confidence intervals. There are other files that also look like they could assess significant differences between dN/dS on branches: BranchClassDNDS.bf, SelectionLRT.bf, TestBranchDNDS.bf, MRPositiveSelection.bf, SubtreeSelectionComparison.bf. I don't quite see their purpose if I can show differences in dNdSBivariateRateAnalysis.bf. Do they differ hugely in assumptions or power? Are they documented anywhere other than the message boards and the HyPhy user manuals?
I have also run FEL on the data to obtain selected codons. Is there an easy way to map inferred substitutions on the tree? Is there a way to map the (dis)appearance of certain motifs on the tree?
Thanks again so much for your help.
Sarah
p.s. Computer froze after 98 h of dNdSRateAnalysis.bf, so I restarted with dNdSBivariateRateAnalysis.bf 15 h ago. Two odd things: first, the program timer isn't running, though the "LF Optimization. Value X and Y evals/sec" changes every hour or two, and there's occasionally movement on the progress bar. Second, the status light remains yellow. I encountered similar issues with CodonModelCompare.bf, except there I had no signs in the first 20 min or so that anything was running after the first min. Is this a problem with my computer (2 Ghz Intel iMac), the latest Universal Binary version of HyPhy, or am I misinterpreting something?