The Conservation track in the Comparative Genomics section of the browser shows genomic sequence alignments of multiple species. We have provided a way to display these multiple alignments for coding regions of genes, either as nucleotides or as amino acids in FASTA format. The tool is available via the Table Browser and from the details pages of the UCSC Genes and RefSeq Genes tracks. In the Table Browser, when a gene prediction track is selected and a multiple alignment is available for the selected species, the option for ‘CDS FASTA alignment from multiple alignment’ appears in the output format menu. Several options are available for formatting the output, including the option to exclude species from the multiple alignment display.
