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/raxml.sh

@@ -0,0 +1,20 @@
+#! /bin/bash
+set -e
+if [ "$#" -ne 4 ]; then
+    echo "Usage: $0 <alignment.fa> <output_prefix> <threads> <outgroup>"
+    echo "Run modeltest-ng and raxml-ng on a given alignment"
+    exit 1
+fi
+
+aln=$(readlink -f "$1")
+out=$2
+threads=$3
+outgroup=$4
+outdir=$(dirname "$out")
+mkdir -p "$outdir"
+# run modeltest-ng
+modeltest-ng -p "$threads" -r 12345 --force -i "$aln" -d nt -t ml -o "$out".modeltest
+# run raxml-ng
+cmd=$(grep "raxml-ng" "$out".modeltest.out | tail -n 1 | sed 's/> //')
+params="--all --bs-trees 1000 --outgroup $outgroup --redo --threads $threads --seed 12345 --prefix $out"
+bash -c "$cmd $params" >/dev/null