usage: diffind-start.py [-h] [-v] [-c C] [-g G] [-s2 S2] --ref REF --files FILES [FILES ...] [--nucleotide] [--odir ODIR] [--threads THREADS] [--donot-skip-zeros] [--donot-skip-non-zeros] [--dendro-file-name DENDRO_FILE_NAME] [--top-font-size TOP_FONT_SIZE] [--filter-value FILTER_VALUE] [--drop-single-zero] [--no-clear]
optional arguments: -h, --help show this help message and exit -v, --version display version number and exit -c Sequence identity threshold -g By cd hit's default algorithm, a sequence is clustered to the first cluster that meet the threshold (fast mode). If set to 1, the program will cluster it into the most similar cluster that meet the threshold(accurate but slow mode) -s2 length difference cutoff for db1, default 1.0 by default, seqs in db1 >= seqs in db2 in a same cluster if set to 0.9, seqs in db1 may just >= 90% seqs in db2 --ref REF Reference file files will be compared with it --files FILES [FILES ...] List of files to be checked against --ref --nucleotide files that are going to be compared are in nucleotide format --odir ODIR dir name where outputed files will be saved --threads THREADS number of threads to use --donot-skip-zeros removing from dendrogram values that are all equal 0 for same label --donot-skip-non-zeros removing from dendrogram values that are all greater then 0 for same label --dendro-file-name DENDRO_FILE_NAME name of pdf file containing ploted dedrogram will be saved in output dir (--odir flag) --top-font-size TOP_FONT_SIZE size of font used to plot gene names on top dendrogram --filter-value FILTER_VALUE drops column if absolute value of difference between max and min in gene less then filter value --drop-single-zero drops column if single zero found --no-clear does not attach numbers to genes names