---
name: "run-sepp.sh"
section: "1"
platform: "linux"
package: "sepp"
version: "4.3.10+dfsg-5"
release: "Debian 11 (Bullseye)"
platforms: ["linux"]
url: "https://new.carta.tech/run-sepp.sh"
---

# run-sepp.sh(1)

a phylogenetic placement tool

## 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)