Usage: dialign-t [OPTIONS] [] -d Debug-Mode [DEFAULT 0] 0 no debug statements 1 debugs the current phase of the processing 2 very loquacious debugging 5 hardcore debugging -s maximum amount of input sequences [DEFAULT 5000] -a maximum number of characters per line in a FASTA file [DEFAULT 100] -c maximum amount of characters per line when printing a sequence [DEFAULT 80] -l sensitivity mode, the higher the level the less likely spurious random fragments are aligned in local alignments [DEFAULT 0] 0 switched off 1 level-1, reduced sensitivity 2 level-2, strongly reduced sensitivity -m score matrix file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM.scr] [DEFAULT DNA: dna_matrix.scr] -w defines the minimum weight when the weight formula is changed to 1-pow(1-prob, factor) [DEFAULT 0.000000065] -p probability distribution file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM.diag_prob_t10] [DEFAULT DNA: dna_diag_prob_100_exp_550000] -v add to each score (to prevent negative values) [DEFAULT 0] -t "even" threshold for low score for sequences alignment [DEFAULT PROTEIN: 4] [DEFAULT DNA: 0] -n maximum number of consecutive positions for window containing low scoring positions [DEFAULT PROTEIN: 4] [DEFAULT DNA: 4] -g global minimum fragment length for stop criterion [DEFAULT PROTEIN: 40] [DEFAULT DNA: 40] -m minimal allowed average score in frag window containing low scoring positions [DEFAULT PROTEIN: 4.0] [DEFAULT DNA: 0.25] -o wether overlap weights are calculated or not [DEFAULT 0] -f minimum fragment length [DEFAULT 1] -r threshold weight to consider the fragment at all [DEFAULT 0.0] -u [DEFAULT 0] 1: only use a sqrt(amount_of_seqs) stripe of neighbour sequences to calculate pairwise alignments (increase performance) 0: all pairwise alignments will be calculated -A optional anchor file [DEFAULT none] -D input is DNA-sequence -T translate DNA into aminoacids from begin to end (length will be cut to mod 3 = 0) WARNING: Do not use -D with this option (Default values for PROTEIN input will be loaded) -L compare only longest Open Reading Frame WARNING: Do not use -D with this option (Default values for PROTEIN input will be loaded) -O translate DNA to aminoacids, reading frame for each sequence calculated due to its longest ORF WARNING: Do not use -D with this option (Default values for PROTEIN input will be loaded) -P output in aminoacids, no retranslation of DNA sequences [DEFAULT: input = output] -F fast mode (implies -l0, since it already significantly reduces sensitivity) -C generate probability table saved in /prob_table and exit -H -h print this message