synolog --ann_type type --org orgstr --annotation path [--agp path] [--org orgstr --annotation path [--agp path] ...] --hits path [--hits_prefix path] -o out_path [--ann_evidence type ...] [-v] [-h]

• -P,--in_path — path to the directory containing the Stacks files.
• -o,--out_path — path to write output files.
• -t,--threads — number of threads to run in parallel sections of code.
• -v — print the version and exit.
• -h — display this help message.
• --ann_type [type] — specify the sequence search program used; 'gtf', 'gzgtf', 'gff' and 'gzgff' supported (default 'gtf').
• --org [org] — specify a string to represent the organism in the output.
• --annotation [path] — path to a genome annotation file.
• --agp [path] — path to a genome structure file providing scaffold/chromosome orders and lengths.
• --ann_evidence [type] — only accept annotation objects with certain underlying evidence; 'rnaseq', 'protein', 'abinitio' are acceptable forms of evidence.
• --hits [path] — path to a file containing the list of sequence search hits to load.
• --hits_prefix [path] — specify a path to the directory containing the sequence search hits files.
• --metric [type] — specify how to rank sequence similarity hits; 'evalue' and 'bitscore' supported (default 'evalue').
• --window_size [size] — specify the size of the sliding window to find conserved syntenic clusters (default 25).
• --merge_mode [type] — specify the method to merge synteny blocks; `strict`, `colinear`, and `overlap` (default `strict`)
• --tree_mode [type] — specify the method to merge synteny blocks across the phylogenetic tree; `pairwise`, `congruent` (default `congruent`)
• --tree — include additional phylogenetic information in newick format to find tandem duplicates.
• --tand_window [size] — specify the size of the sliding window to find tandem duplicates (default 15).
• --min_elements [size] — specify the minimum number of elements to form a synteny cluster (default 2).
• --perc_id [float] — specify the minimum percent identity required to keep a blast hit in the analysis (default 0.0).
• --bit_stdev [float] — specify the number of standard deviations from the top bit score to consider a blast hit similar (default 0.5).
• --verbose — display additional information in error cases.