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.

99.scripts/miscs/mcmctree.ctl

@@ -0,0 +1,32 @@
+          seed = 12345
+       seqfile = input.fa
+      treefile = input.tre
+       outfile = {{PREFIX_PLACEHOLDER}}.mcmctree.out
+
+         ndata = 1
+       seqtype = 0  * 0: nucleotides; 1:codons; 2:AAs
+       usedata = 1    * 0: no data; 1:seq like; 2:use in.BV; 3: out.BV
+         clock = 3    * 1: global clock; 2: independent rates; 3: correlated rates
+       RootAge = <100  * safe constraint on root age, used if no fossil for root.
+
+         model = {{MODEL_PLACEHOLDER}}    * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
+         alpha = {{GAMMA_PLACEHOLDER}}    * alpha for gamma rates at sites
+         ncatG = 4    * No. categories in discrete gamma
+
+     cleandata = 0    * remove sites with ambiguity data (1:yes, 0:no)?
+
+       BDparas = 1 1 0.1 C    * birth, death, sampling
+   kappa_gamma = 6 2      * gamma prior for kappa
+   alpha_gamma = 1 1      * gamma prior for alpha
+
+   rgene_gamma = 2 2   * gamma prior for overall rates for genes
+  sigma2_gamma = 1 10    * gamma prior for sigma^2     (for clock=2 or 3)
+
+      finetune = 1: 0.1  0.1  0.1  0.01 .5  * auto (0 or 1) : times, musigma2, rates, mixing, paras, FossilErr
+
+         print = 2
+        burnin = 200000
+      sampfreq = 200
+       nsample = 5000
+
+*** Note: Make your window wider (100 columns) before running the program.