]> Align nucleic coding regions given the aligned proteins (EMBOSS) alignment:multiple http://bioweb.pasteur.fr/docs/EMBOSS/tranalign.html tranalign &emboss_init; input Input section asequence asequence -- nucleotide [sequences] (-asequence) perl " -asequence=$value -sformat=fasta" 1 nucleotide 8 seqsfile perl 1 bsequence bsequence -- gapprotein [set of sequences] (-bsequence) perl " -bsequence=$value -sformat=fasta" 2 gapprotein 8 advanced Advanced section table Code to use -- Genetic codes (-table) 0 Standard 1 Standard (with alternative initiation codons) 2 Vertebrate Mitochondrial 3 Yeast Mitochondrial 4 Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma 5 Invertebrate Mitochondrial 6 Ciliate Macronuclear and Dasycladacean 9 Echinoderm Mitochondrial 10 Euplotid Nuclear 11 Bacterial 12 Alternative Yeast Nuclear 13 Ascidian Mitochondrial 14 Flatworm Mitochondrial 15 Blepharisma Macronuclear 16 Chlorophycean Mitochondrial 21 Trematode Mitochondrial 22 Scenedesmus obliquus 23 Thraustochytrium Mitochondrial 0 perl " -table=$value" 3 output Output section outseq outseq -- gapnucleotide (-outseq) outseq.out perl " -outseq=$value" 4 seqsfile perl 1 outseq_sformat Output format for: outseq -- gapnucleotide fasta fasta gcg gcg phylip phylip embl embl swiss swiss ncbi ncbi nbrf nbrf genbank genbank ig ig codata codata strider strider acedb acedb staden staden text text fitch fitch msf msf clustal clustal phylip phylip phylip3 phylip3 asn1 asn1 fasta perl " -osformat=$value" 5 auto perl " -auto -stdout" 6