codon usage table, distance matrix and bases composition Pesole, Attimonelli and Liuni Graziano Pesole, Marcella Attimonelli and Sabino Liuni (CNR-Bari). NAR (16):5:1988 pp. 1715-1728 codontree codontree seqlab codontree perl "codontree" 0 seqfile Sequences File perl " $value" 1 8 files *.tab *.bc *.mat tabfile perl " -TABfile=$seqfile.tab" 3 control_options Control options 2 ntable Translation table to be used for the computation of distance and codon usage (-NTAble) perl ($value && $value ne $vdef)? " -NTAble=$value" : "" 0 2 0 UNIVERSAL 1 CILIATED PROTOZOA 2 DROSOPHILA MITOCHONDRIAL 3 MAMMALIAN MITOCHONDRIAL 4 YEAST MITOCHONDRIAL output_options Output options 2 bc Bases composition to be computed (-BC) perl ($value)? " -BC=$value" : "" 2 1 -BC=1 prints the bases composition values of the first position of codons 2 -BC=2 prints the bases composition values of the second position 3 -BC=2 prints the bases composition values of the third position A -BC=A prints the bases composition values of all the three Q -BC=Q prints the bases composition values of quartets '' eachseq Allows the printout of a distinct codon usage table for each sequence of the input file (-EACHseq) perl ($value)? " -EACHseq" : "" 2 If the switch is not on the command line, the codon usage table refers to all sequences in the input file. dist Allows the computation and the printout of the distances matrix (-DISTance) perl ($value)? " -DISTance" : "" 2 verbose Prints on the screen some useful information (-VERbose) perl ($value)? " -VERbose" : "" 2 bcfile perl " -BCFILE=$seqfile.bc" 3 perl $bc matfile perl " -MATFILE=$seqfile.mat" 3 perl $dist