2.0 Align DNA sequences corresponding to a protein alignment K. Schuerer, C. Letondal protal2dna protal2dna perl "protal2dna" 0 outfile "protal2dna.out" readseq_ok_alig perl 1 alig Protein alignment perl " $value" 100 100 readseq_ok_alig perl 1 dna DNA Sequences File perl " $value" 101 The DNA sequences must contain at least the region coding for each sequence of the protein alignment. 8 fasta perl "mv $dna $dna.in ; fasta2fasta $dna.in > $dna ; " -10 same_ids Identify corresponding DNA sequences by same ID or name (-i) perl ($value && $value ne $vdef) ? " -i" : "" 0 1 The correspondance between protein and DNA sequences may be based on their position in the files or by their name. outformat Output Alignment Format perl ($value && $value ne $vdef) ? " -f $value" : "" clustalw 1 fasta Pearson/Fasta pfam Pfam msf MSF clustalw Clustalw genetic Default Genetic Code (-g) perl ($value && $value ne $vdef) ? " -g $value" : "" 1 1 1 Standard 2 Vertebrate Mitochondrial 3 Yeast Mitochondrial 4 Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma 5 Invertebrate Mitochondrial 6 Ciliate Macronuclear and Dasycladacean 9 Echinoderm Mitochondrial 10 Euplotid Nuclear 11 Bacterial 12 Alternative Yeast Nuclear 13 Ascidian Mitochondrial 14 Flatworm Mitochondrial 15 Blepharisma Macronuclear speccode Special Genetic Code (-G) perl ($value) ? " -G $value" : "" 1 File containing genetic code numbers of sequences that differs from the default code used. Format: one special code per line with prot-id used in the alignment followed by the code number