Scripts to extract multiple alignments of ORF sequences, reconstruct ancestral sequences, evaluate the sequence conservation of ORFs and trace similar proteins across the included species.
bash pipeline.sh [BED ORFs 1-based] [folder with MAF alignments: chr1.maf, chr2.maf...] [output folder] [nwk file] [FASTA ORF proteins]
Adjusted from https://github.com/jorruior/riboseq_orfs_analyses