Add MCMCtree workflow and SNaQ analysis scripts

- Updated `pixi.toml` to include new R package dependencies for MCMCtree workflow.
- Modified markdown file to remove unnecessary simulation data discussion.
- Introduced `.lintr` configuration for linting R scripts.
- Created `mcmctree.ctl` control file for MCMCtree analysis.
- Developed `mcmctree_workflow.r` script to orchestrate MCMCtree analysis with model testing and ESS checks.
- Added `06.snaq.jl` script for SNaQ analysis with plotting capabilities.
- Implemented `07.mcmctree.sh` bash script to run MCMCtree on multiple alignments in parallel.

pixi.toml

@@ -52,6 +52,10 @@ paml = ">=4.10.9,<5"
 beagle-lib = "==3.1.2"
 mrbayes = ">=3.2.7,<4"
 cairosvg = ">=2.8.2,<3"
+r-devtools = ">=2.4.6,<3"
+r-phytools = ">=2.5_2,<3"
+r-argparser = ">=0.7.2,<0.8"
+r-processx = ">=3.8.6,<4"
 
 [feature.beast.dependencies]
 beagle-lib = ">=4.0.1,<5"