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/workflow/phylogeny_reconstruction/07.mcmctree.sh

@@ -0,0 +1,29 @@
+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+THREADS=${THREADS:-16}
+
+if [ "$#" -ne 4 ]; then
+    echo "Usage: $0 <aln_dir> <ml_dir> <out_dir> <alignment_ext>"
+    echo "Run MCMCtree on orthogroup alignments with corresponding ML trees"
+    exit 1
+fi
+
+aln_dir=$1
+ml_dir=$2
+out_dir=$3
+ext=$4
+mkdir -p "$out_dir"
+echo -n >mcmctree.cmds
+ctlfile=$(readlink -f "$SCRIPTS/miscs/mcmctree.ctl")
+for i in "$aln_dir"/*."$ext"; do
+    j=$(basename "$i" ."$ext")
+    aln=$(readlink -f "$i")
+    ml_tree=$(readlink -f "$ml_dir/${j}/${j}.raxml.bestTree")
+    mkdir -p "${out_dir}/${j}"
+    cmd="cd ${out_dir}/${j} && Rscript $SCRIPTS/miscs/mcmctree_workflow.r"
+    params="-a $aln -t $ml_tree -c ${ctlfile} -p ${j}"
+    echo "$cmd $params > mcmctree.log 2>&1" >>mcmctree.cmds
+done
+xargs -t -P "$THREADS" -I cmd -a mcmctree.cmds bash -c "cmd"
+echo "MCMCtree all completed."