1.0 Comparison of coding DNA Pedersen, Lyngso,Hein Christian N. S. Pedersen, Rune B. Lyngso and Jotun Hein. Comparison of coding DNA in Proceedings of the 9th Annual Symposium of Combinatorial Pattern Matching (CPM), 1998. alignment:multiple combat combat perl "cat $sequence2 >> $sequence1; combat control_file > distance.out ; combat_combine $sequence1 combat.aln" 0 sequence1 First Sequence perl ">inputfile\n\"$value\"\n" 8 1 control_file Each of the two sequences must describe an integer number of codon, i.e. the length of each sequence must be a multiple of three. sequence2 Second Sequence perl "" 8 0 Each of the two sequences must describe an integer number of codon, i.e. the length of each sequence must be a multiple of three. output_aln "combat.aln" perl ">outputfile\n\"combat.aln\"\n" 2 control_file alignment_file "combat.out" perl "" 0 readseq_ok_alig perl 1 protein_distance_matrix Amino-acid distance matrix PAM60 PAM60 PAM120 PAM120 PAM250 PAM250 PAM350 PAM350 Blosum30 Blosum30 Blosum62 Blosum62 Blosum90 Blosum90 PAM60 perl ">distance matrix\n\"/local/gensoft/lib/combat/$value" . "_distance.m\"\n" 3 control_file nucleotide_distance_matrix Nucleotid distance matrix 1 matrix 1 2 matrix 2 3 matrix 3 1 perl ">nucleotide matrix\n\"/local/gensoft/lib/combat/nucleotide_distance$value.m\"\n" 4 control_file protein_gap_open Gap open cost for protein perl ">gap functions\\nprotein: $value" 20 5 control_file protein_gap_ext Gap extension cost for protein perl " + $value*k\\n" 8 6 control_file dna_gap_open Gap open cost for dna perl "dna: $value" 8 7 control_file dna_gap_ext Gap extension cost for dna perl " + $value*k" 2 8 control_file results_files control_file gnuplot_file combat.ps distance.out gnuplot_call perl "; gnuplot < gnuplot_file" 100 gnuplot_commands perl "set xtics 12,5.,1000\nset ytics 12,5.,1000\nset grid\nset terminal postscript\nset output \"combat.ps\"\nplot \"combat.aln\" with lines\n" 1 gnuplot_file