Add scripts for phylogenetic analysis using MrBayes and RAxML

- Created `mbblock.txt` for MrBayes configuration.
- Implemented `mrbayes.sh` to convert FASTA to Nexus and run MrBayes.
- Developed `raxml.sh` to run modeltest-ng and raxml-ng on alignments.
- Added `04.filter_ogs.sh` to filter orthologous groups based on taxon count and sequence length.
- Implemented `01.run_mrbayes.sh` to execute MrBayes for multiple FASTA files.
- Created `02.mbsum.sh` to summarize MrBayes output while skipping high DSF analyses.
- Developed `03.run_raxml.sh` to run raxml-ng on filtered alignments.

99.scripts/workflow/phylogeny_reconstruction/01.run_mrbayes.sh

@@ -0,0 +1,21 @@
+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <input_fasta_dir> <extension> <output_dir>"
+    echo "Run MrBayes for each fasta file in the input directory"
+    exit 1
+fi
+
+input_dir=$(readlink -f "$1")
+ext=$2
+output_dir=$(readlink -f "$3")
+mkdir -p "${output_dir}"
+echo -n >mrbayes.cmds
+for f in "${input_dir}"/*."${ext}"; do
+    j=$(basename "$f" ."${ext}")
+    echo "bash $SCRIPTS/miscs/mrbayes.sh $f ${output_dir}/${j}/${j}.nex" >>mrbayes.cmds
+done
+xargs -t -P 12 -I cmd -a mrbayes.cmds bash -c "cmd"
+echo "All MrBayes analyses are done!"