How do I get alignments of homologous proteins? Can I get the CDS (coding sequence) alignments as well? I'm using the API.
Yes, both can be obtained using the Compara API: see this example script.
Protein alignments of homologues are also available using the orthologues or paralogues links from the Gene tab in the browser. The link at the bottom of the page allows a customised view of the protein alignments.