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