20261002

99.scripts_v2/utils/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="--blopt nr_safe --all --bs-trees 1000 --outgroup $outgroup --redo --threads $threads --seed 12345 --prefix $out"
+bash -c "$cmd $params" >/dev/null