run-sepp.sh1
A phylogenetic placement tool
Overview
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
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-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]
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-a ALIGN, --referenceAlignment ALIGN -
Aligned fasta file [default: None]
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-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
-x8 to make SEPP us 8 threads