harvesttools - archiving and postprocessing for reference-compressed genomic multi-alignments

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

harvesttools 1.2                                   March 2016                                    HARVESTTOOLS(1)

       Harvesttools  is  a  utility  for creating and interfacing with Gingr files, which are efficient archives
       that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees,  filtered
       variants  and  annotations.  Though designed for use with Parsnp and Gingr, HarvestTools can also be used
       for generic conversion between standard bioinformatics file formats.

       harvesttools - archiving and postprocessing for reference-compressed genomic multi-alignments

-i <Gingr input>

       -b <bed filter intervals>,<filter name>,"<description>"

       -B <output backbone intervals>

       -f <reference fasta>

       -F <reference fasta out>

       -g <reference genbank>

       -a <MAF alignment input>

       -m <multi-fasta alignment input>

       -M <multi-fasta alignment output (concatenated LCBs)>

       -n <Newick tree input>

       -N <Newick tree output>

       --midpoint-reroot (reroot the tree at its midpoint after loading)

       -o <Gingr output>

       -S <output for multi-fasta SNPs>

       -u 0/1 (update the branch values to reflect genome length)

       -v <VCF input>

       -V <VCF output>

       -x <xmfa alignment file>

       -X <output xmfa alignment file>

       -h (show this help)

       -q (quiet mode)

harvesttools <options>