Multiple codon alignments of orthologs inferred with TOGA2. 
The alignments were generated with the "codonification" procedure. 
The species tree, which we used as a guide tree for the alignments, is provided in speciesTree.nh file in Newick format.

The subfolders specify the reference species used in TOGA2. 
We included both 1:1 and many:1 orthologs, meaning the query species has exactly one ortholog. 

The assemblies, including information such as assembly source, accession, N50s, species names and taxonomy, is given in 
  ../assemblies_and_species.tsv

In the alignment, N's denote bases that were masked, either because they are part of a frame-shifted query codon or because they belong to a complete query codon located between two compensating frameshifts. Sequence regions downstream of frameshifts are also masked with Ns, because selective constraints may act on a reading frame that differs from the reference frame. 
Dashes (-) refer to insertions/deletions.