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/06.alignments_to_nexus.sh

@@ -1,18 +0,0 @@
-#! /usr/bin/env bash
-
-if [ "$#" -ne 3 ]; then
-    echo "Usage: $0 <input_fasta_dir> <extension> <output_nexus_dir>"
-    exit 1
-fi
-
-input_dir=$1
-extension=$2
-output_dir=$3
-mkdir -p "${output_dir}"
-for f in "${input_dir}"/*."${extension}"; do
-    filename=$(basename -- "${f}")
-    filename_noext="${filename%.*}"
-    output_file="${output_dir}/${filename_noext}.nex"
-    echo "Converting ${f} to ${output_file}"
-    seqmagick convert --output-format nexus --alphabet dna --input-format fasta "${f}" "${output_file}"
-done

99.scripts/workflow/phylogeny_reconstruction/06.snaq.jl

@@ -104,10 +104,10 @@ R"dev.off"();
 
 ## expected vs. observed quartet concordance factors
 using CSV, DataFrames, Distributions, Random, RCall;
-inputCFfile = joinpath("bucky_1.CFs.csv");
+inputCFfile = joinpath("..","bucky","bucky_1","input.mb.CFs.csv");
 inputCF = readtableCF(inputCFfile);
-net3 = readsnaqnetwork("net3.out");
-topologymaxQpseudolik!(net3, inputCF);
+net4 = readsnaqnetwork("net4.out");
+topologymaxQpseudolik!(net4, inputCF);
 df_long = fittedquartetCF(inputCF, :long);
 
 ### Adding jitter to the points for better visualization
@@ -127,6 +127,6 @@ R"dev.off"();
 
 # Goodness of fit of the SNaQ networks
 using QuartetNetworkGoodnessFit;
-res1 = quarnetGoFtest!(net3, inputCF, true; seed=123, nsim=1000);
+res1 = quarnetGoFtest!(net4, inputCF, true; seed=123, nsim=1000);
 res1[[1,2,3]] # p-value, uncorrected z, σ
 

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."