NAME

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

SYNOPSIS

       harvesttools <options>

DESCRIPTION

       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.

OPTIONS

       -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)

AUTHOR

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