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/03.run_raxml.sh

@@ -0,0 +1,23 @@
+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+THREADS=${THREADS:-4}
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <in_dir> <out_dir> <ext>"
+    echo "Run raxml-ng on filtered orthogroup alignments"
+    exit 1
+fi
+
+in_dir=$(readlink -f "$1")
+out_dir=$2
+ext=$3
+mkdir -p "$out_dir"
+echo -n >raxml.cmds
+for i in "$in_dir"/*."$ext"; do
+    j=$(basename "$i" ."$ext")
+    out_prefix="$out_dir/${j}/${j}"
+    echo "$SCRIPTS/miscs/raxml.sh $i $out_prefix 4 Zju" >>raxml.cmds
+done
+xargs -t -P "$THREADS" -I cmd -a raxml.cmds bash -c "cmd"
+echo "Raxml-ng all completed."