NAME

       run-sepp.sh - a phylogenetic placement tool

DESCRIPTION

       usage:  run-sepp.sh  [input  fragments file] [output prefix] [-x N] [-A ALIGN] [-P N] [any
       other SEPP argument] [-t TREE] [-a ALIGN] [-r RAXML] [-n argN] [-b argB]

   OPTIONS
       -x N, --cpu N
              Use N cpus [default: number of cpus available on the machine]

       -A ALIGN, --alignmentSize ALIGN
              max alignment subset size of ALIGN [default: 10% of the total number of taxa or the
              placement subset size if given]

       -P N, --placementSize N
              max  placement  subset  size  of N [default: 10% of the total number of taxa or the
              alignment length (whichever bigger)]

       -t TREE, --referencePhylogeny TREE
              Input tree file (newick format) [default: None]

       -a ALIGN, --referenceAlignment ALIGN
              Aligned fasta file [default: None]

       -r RAXML, --referenceInfoFile RAXML
              RAxML_info file including model parameters, generated by RAxML.[default: None]

       -n argN, --noTreeComputation argN
              if set to something (for instance  1),  no  tree  computation  is  made,  just  the
              placements one.

       -b argB, --debugInformation argB
              If set to something (for instance 1), report debugging information.

              Optional  commands  need  not  be in order. Any SEPP option can also be passed. For
              example, use -x 8 to make SEPP us 8 threads

SEE ALSO

       run_sepp.py(5)