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/miscs/mrbayes.sh

@@ -0,0 +1,20 @@
+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+
+if [ "$#" -ne 2 ]; then
+    echo "Usage: $0 <input_fasta> <output_nexus>"
+    exit 1
+fi
+
+in_fasta=$(readlink -f "$1")
+out_nex=$2
+
+# Convert fasta to nexus
+out_dir=$(dirname "$out_nex")
+mkdir -p "$out_dir"
+seqmagick convert --output-format nexus --alphabet dna --input-format fasta "$in_fasta" "$out_nex"
+# append MrBayes block to nexus file
+cat "$SCRIPTS"/miscs/mbblock.txt >>"$out_nex"
+# Run MrBayes
+mb "$out_nex" >"${out_dir}"/mrbayes.log 2>&1