Alignment free sequence comparison synopsis alf [options] -i in.fasta [-o out.txt] description compute pairwise similarity of sequences using alignment-free methods in in.fasta and write out tab-delimited matrix with pairwise scores to out.txt. -h, --help displays this help message. --version display version information -v, --verbose when given, details about the progress are printed to the screen. input / output: -i, --input-file file name of the multi-fasta input file. valid filetypes are: fa and fasta. -o, --output-file file name of the file to which the tab-delimtied matrix with pairwise scores will be written to. default is to write to stdout. valid filetype is: alf.tsv. general algorithm parameters: -m, --method method select method to use. one of n2, d2, d2star, and d2z. default: n2. -k, --k-mer-size k size of the k-mers. default: 4. -mo, --bg-model-order order order of background markov model. default: 1. n2 algorithm parameters: -rc, --reverse-complement mode which strand to score. use both_strands to score both strands simultaneously. one of input, both_strands, mean, min, and max. default: input. -mm, --mismatches mismatches number of mismatches, one of 0 and 1. when 1 is used, n2 uses the k-mer-neighbour with one mismatch. default: 0. -mmw, --mismatch-weight weight real-valued weight of counts for words with mismatches. default: 0.1. -kwf, --k-mer-weights-file file.txt print k-mer weights for every sequence to this file if given. valid filetype is: txt. contact and references for questions or comments, contact: jonathan goeke [email protected] please reference the following publication if you used alf or the n2 method for your analysis: jonathan goeke, marcel h. schulz, julia lasserre, and martin vingron. estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. bioinformatics (2012). project homepage: http://www.seqan.de/projects/alf version alf version: 1.1 last update january 5, 2012