PAML ancestral sequences reconstruction

Question

[ulises.rodriguez]

Hello,

I have a set of about 9,000 groups of orthologous proteins I'm trying to do ancestral sequence reconstructions for each of these groups based on their phylogenies, and then to compare each nucleotide position in a species of interest to the reconstructed sequences at key ancestral nodes.

I've been trying to use PAML (codeml) for this task, but I do not know if is there a way to do this task in a automated, I mean, a way to do a control file for both each alignment and tree file, I have done the multiple sequence aligment with muscle and the tree inference with IQtree, but I'm stuck with the next part with codeml. I did use the next code to do the MSA with muscle .

#PBS -N aa_anc_seq_aln
#PBS -l nodes=1:ppn=1,mem=32gb,vmem=32gb,walltime=25:00:00
#PBS -q default
#PBS -V

cd working_directory     
module load  muscle/3.8.31

for file in *.fna; do muscle -in $file -out "${file/.fna/_aln.fna}"; done

[Juke34]

You could use a tool like Ortheus[1] to perform an ancestral sequence reconstruction from the sequence alignment done for each ortholog group.

[1] Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, et al. (2008) Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Research 18: 1829–1843.