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.gitignore
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## Old files
z_old
## VScode files
.vscode
00_data_formatting/.vscode
## Unnecessary raw pptx/docx files
02_additional_figs_tables/*pptx
02_additional_figs_tables/*docx
## Files too big to push for core analyses
01_PAML/*MCMCtree*/out_RData
01_PAML/*MCMCtree*/sum_analyses/00_prior/CLK/*/mcmc.txt
01_PAML/*MCMCtree*/sum_analyses/00_prior/mcmcf4traces*
01_PAML/*MCMCtree*/sum_analyses/00_prior/mcmc_files_*/mcmc.txt
01_PAML/*MCMCtree*/sum_analyses/01_posterior/*/*/mcmc.txt
01_PAML/*MCMCtree*/sum_analyses/01_posterior/mcmc_files_*/mcmc.txt
01_PAML/*MCMCtree*/sum_analyses/01_posterior/mcmcf4traces*
01_PAML/*MCMCtree*/sum_files_prior/margVScalib/*/*tif
01_PAML/*MCMCtree*/sum_files_prior/margVScalib/*/ind/*tif
01_PAML/*MCMCtree*/plots/margVScalib/*/*tif
01_PAML/*MCMCtree*/plots/margVScalib/*/ind/*tif
01_PAML/figs_tables/out_RData
## Files too big to push for analyses with single-gene alignments
03_additional_analyses/01_lou_analyses/src/fasta-phylip-partitions
03_additional_analyses/00_indgenes_analyses/01_PAML/00_MCMCtree/out_RData/
03_additional_analyses/00_indgenes_analyses/01_PAML/00_MCMCtree/sum_analyses/00_prior/CLK/*/*/mcmc.txt
03_additional_analyses/00_indgenes_analyses/01_PAML/00_MCMCtree/sum_analyses/00_prior/mcmc_files_*/mcmc.txt
03_additional_analyses/00_indgenes_analyses/01_PAML/00_MCMCtree/sum_analyses/00_prior/mcmcf4traces*
03_additional_analyses/00_indgenes_analyses/01_PAML/00_MCMCtree/sum_analyses/01_posterior/mcmc_files_*/mcmc.txt
03_additional_analyses/00_indgenes_analyses/01_PAML/00_MCMCtree/sum_analyses/01_posterior/*/*/*/mcmc.txt
03_additional_analyses/00_indgenes_analyses/01_PAML/00_MCMCtree/sum_analyses/01_posterior/mcmcf4traces*
03_additional_analyses/00_indgenes_analyses/01_PAML/00_MCMCtree/plots/margVScalib/*/*tif
03_additional_analyses/00_indgenes_analyses/01_PAML/00_MCMCtree/plots/margVScalib/*/ind/*tif
03_additional_analyses/00_indgenes_analyses/01_PAML/00_MCMCtree/sum_files_prior/margVScalib/*/ind/*tif
03_additional_analyses/00_indgenes_analyses/01_PAML/00_MCMCtree/sum_files_prior/margVScalib/*/*tif
## Files too big to push for "leave-one-out" analyses
03_additional_analyses/01_lou_analyses/LUCA-divtimes_no*/01_PAML/01_MCMCtree/out_RData
03_additional_analyses/01_lou_analyses/LUCA-divtimes_no*/01_PAML/01_MCMCtree/sum_analyses/00_prior/mcmc_files_*/mcmc.txt
03_additional_analyses/01_lou_analyses/LUCA-divtimes_no*/01_PAML/01_MCMCtree/sum_analyses/00_prior/mcmcf4traces*
03_additional_analyses/01_lou_analyses/LUCA-divtimes_no*/01_PAML/01_MCMCtree/sum_analyses/00_prior/CLK/*/mcmc.txt
03_additional_analyses/01_lou_analyses/LUCA-divtimes_no*/01_PAML/01_MCMCtree/sum_analyses/01_posterior/mcmc_files_*/mcmc.txt
03_additional_analyses/01_lou_analyses/LUCA-divtimes_no*/01_PAML/01_MCMCtree/sum_analyses/01_posterior/*/*/mcmc.txt
03_additional_analyses/01_lou_analyses/LUCA-divtimes_no*/01_PAML/01_MCMCtree/sum_analyses/01_posterior/mcmcf4traces*
03_additional_analyses/01_lou_analyses/LUCA-divtimes_no*/01_PAML/01_MCMCtree/plots/margVScalib/*/*tif
03_additional_analyses/01_lou_analyses/LUCA-divtimes_no*/01_PAML/01_MCMCtree/plots/margVScalib/*/ind/*tif
03_additional_analyses/01_lou_analyses/LUCA-divtimes_no*/01_PAML/01_MCMCtree/sum_files_prior/margVScalib/*/ind/*tif
03_additional_analyses/01_lou_analyses/LUCA-divtimes_no*/01_PAML/01_MCMCtree/sum_files_prior/margVScalib/*/*tif
## Files too big to push for "leave-one-out" analyses
03_additional_analyses/02_blunc_analysis/02_PAML/MCMCtree/out_RData
03_additional_analyses/02_blunc_analysis/02_PAML/MCMCtree/sum_analyses/01_posterior/*/*/mcmc.txt
03_additional_analyses/02_blunc_analysis/02_PAML/MCMCtree/sum_analyses/01_posterior/mcmc_files*/mcmc.txt
03_additional_analyses/02_blunc_analysis/02_PAML/MCMCtree/sum_analyses/01_posterior/mcmcf4traces*
## Large compressed file with all the repo
LUCAdivtimes.zip