#Supplementary File S3 : Phylogenomic analyses

#Only complete, single copy BUSCO proteins that were present in all 22 genomes were used for the phylogenomic analyses (n=783)

#Align protein sequences using Muscle v3.8.31
for f in *.fasta; do muscle -in ${f} -out ${f/.fasta/}_muscle.faa; done

#Trim alignments using trimAl v1.4.rev22
for f in *muscle.faa; do trimal -in ${f} -out ${f/_muscle.faa/}_trimal.faa  -automated1; done

#Generate single gene trees using IQtree v1.6.12 
for f in *trimal.faa; do iqtree -s ${f} -bb 1000 -nt 4 -wbt ; done

#Concatenate IQtrees into a single file & generate a file with the names of the files containing bootstrapped trees
cat *.treefile > best.trees
ls *.ufboot > bs_info.txt

#Infer species tree using ASTRAL v5.6.3  
java -jar path.to.Astral/astral.5.6.3.jar -i best.trees -b bs_info.txt -o astral.tree 2> astral.log