Align nucleic coding regions given the aligned proteins emboss tranalign -asequence $input1 -bsequence $input2 -outseq $out_file1 -table $table -osformat3 $out_format1 -auto Nucleic Sequences Protein Sequences Code to use Standard Standard (with alternative initiation codons) Vertebrate Mitochondrial Yeast Mitochondrial Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma Invertebrate Mitochondrial Ciliate Macronuclear and Dasycladacean Echinoderm Mitochondrial Euplotid Nuclear Bacterial Alternative Yeast Nuclear Ascidian Mitochondrial Flatworm Mitochondrial Blepharisma Macronuclear Chlorophycean Mitochondrial Trematode Mitochondrial Scenedesmus obliquus Thraustochytrium Mitochondrial Output Sequence File Format FASTA (m) ACeDB (m) ASN.1 (m) Clustal (m) CODATA (m) EMBL (m) Fitch (m) Wisconsin Package GCG 9.x and 10.x (s) GENBANK (m) GFF (m) Hennig86 (m) Intelligenetics (m) Jackknifer (m) Jackknifernon (m) Mega (m) Meganon (m) Wisconsin Package GCG's MSF (m) NBRF (PIR) (m) NCBI style FASTA (m) Nexus/PAUP (m) Nexusnon/PAUPnon (m) PHYLIP interleaved (m) PHYLIP non-interleaved (m) SELEX (m) Staden (s) DNA strider (m) SwisProt entry (m) Plain sequence (s) Treecon (m)

You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tranalign.html