run-sepp.sh - a phylogenetic placement tool
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]
- -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