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)