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@sabifo4 sabifo4 released this 12 Jul 09:41
LUCAdivtimes-v1.0.1
04b568c

In this release, you will find the step-by-step tutorial with all the guidelines you need to follow to reproduce the results for the timetree inference analyses we carried out as part of our study: The nature of the Last Universal Common Ancestor and its impact on the early Earth system.

I have updated the following content if compared to the pre-release version that we made available while our manuscript was under review:

  • Fixed all typos and broken links that I could find -- I apologise if I have missed some! If you find typos/broken links, please open an issue so that I can fix them, thank you!
  • Updated the comments with instructions to run the various commands in the R scripts that users will need to run to reproduce our results. In essence, some comments were outdated and/or were part of an old PAML tutorial. Now, they have been updated following the comments and instructions I have in similar scripts in my latest MCMCtree tutorial.
  • Included the data for the initial paralogues that were filtered prior to timetree inference (i.e., see raw_8pars_dat and the first paragraph in the corresponding README.md file for more details).
  • Added some tsv files that were ignored.
  • Added additional rows in the Calibnodes* files inside the calib_files directories (i.e., MCMCtree analyses) so that the plots with marginal densities VS calibration densities were also generated for cross-braced nodes. These new plots were generated for all the *MCMCtree directories inside directory 01_PAML and for those under 03_additional_analyses/00_indgenes_analyses as a safety check (i.e., they should be the same for all cross-braced nodes, and they are). Given that there were no issues identified and the safety check was passed, I decided to not add more files in this repository as it already takes a while to index all the files and commit changes. To this end, directories inside 01_lou_analyses and 02_blunc_analysis will have these plots for the first instance of nodes that are cross-braced (i.e., mirror nodes but not driver nodes) as they are essentially the same. Therefore, the Calibnodes* files have remained unchanged.
  • Incorporated the link to the archive we stored at the University of Bristol data repository (~71Gb). Please note that this archive contains the same files that we have in the pre-release, and so the content may have been updated after I carried out the changes aforementioned.

If you use any of the resources in this GitHub repository for your own analyses, please cite the following:

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