You can now get gene ortholog data using the NCBI Datasets command-line tool using a gene ID, gene symbol, or RefSeq nucleotide or protein accession. Data are available for vertebrates and insects. The vertebrate orthologs includes a specialized set for fish. (See our recent post for more information on the orthologs for fish and insects.)
You can retrieve metadata for gene orthologs in JSON Format, or you can download a compressed (zip) archive containing both metadata and sequences (Figure 1).
Figure 1. Command-lines that use a gene symbol (BRCA1) to retrieve mammalian ortholog metadata (top, JSON metadata shown in part in the image) and sequences (bottom).