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RUN-SEPP.SH(1) User Commands RUN-SEPP.SH(1)

NAME - a phylogenetic placement tool


usage: [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]


Use N cpus [default: number of cpus available on the machine]
max alignment subset size of ALIGN [default: 10% of the total number of taxa or the placement subset size if given]
max placement subset size of N [default: 10% of the total number of taxa or the alignment length (whichever bigger)]
Input tree file (newick format) [default: None]
Aligned fasta file [default: None]
RAxML_info file including model parameters, generated by RAxML.[default: None]
if set to something (for instance 1), no tree computation is made, just the placements one.
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


September 2021