Input preparation

Make sure the current directory is captus_work. Before we run the phylogenetic analysis, we need to trim our sequences using trimAl. Install trimAl if it has not been installed in the system.

Make directory output

mkdir -p 04_alignments/03_trimmed/06_informed/01_coding_NUC/03_genes_trimAL 

Trim using automated1 setting

for f in 04_alignments/03_trimmed/06_informed/01_coding_NUC/03_genes/*; do
  base=$(basename "$f")
  trimal -in "$f" \
         -out "04_alignments/03_trimmed/06_informed/01_coding_NUC/03_genes_trimAL/$base" \
         -automated1
done

IQTREE Analysis

Build gene trees for each gene

mkdir -p 04_alignments/03_trimmed/06_informed/01_coding_NUC/iqtree_gene_output
for file in 04_alignments/03_trimmed/06_informed/01_coding_NUC/03_genes_trimAL/*.fna
do
    base=$(basename "$file" .fna)

    iqtree \
        -s "$file" \
        -m MFP \
        -bb 1000 \
        -nt 8 \
        -pre "04_alignments/03_trimmed/06_informed/01_coding_NUC/iqtree_gene_output/$base"
done

Concatanate gene tree files into a single file

cat 04_alignments/03_trimmed/06_informed/01_coding_NUC/iqtree_gene_output/*.treefile > 04_alignments/03_trimmed/06_informed/01_coding_NUC/all_gene_trees.tre

mkdir -p 04_alignments/03_trimmed/06_informed/01_coding_NUC/astral_tree