Comparisons of alignments obtained in codon and amino acid space.

We assessed the concordance between alignments obtained in nucleotide and amino acid space by aligning all 1,502 genes in Saccharomyces cerevisiae which have orthologs in the six related yeast species S. paradoxus, S. mikatae, S. kudriavzevii, S. bayanus, S. castellii, and S. kluyveri (this dataset was analyzed in [5]). Alignments produced by FSA, in both anchored and unanchored (�Cnoanchored) modes, had the highest concordance. Alignment similarity between alignments computed in nucleotide and amino acid space was assessed by converting the amino acid alignment to the implied nucleotide alignment and computing the alignment similarity (the proportion of identical homology statements made by the alignments; see Text S1, ��The mathematics of distance-based alignment�� for details) between them. Alignments for ProbCons on nucleotide sequences were obtained with ProbConsRNA.