---
name: "run_gubbins"
section: "1"
platform: "linux"
package: "gubbins"
version: "3.4-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/run_gubbins"
---

# run\_gubbins(1)

phylogenetic analysis of genome sequences

## NAME

run\_gubbins - phylogenetic analysis of genome sequences

## SYNOPSIS

**run\_gubbins** \[-h\] \[--outgroup OUTGROUP\] \[--starting\_tree STARTING\_TREE\] \[--use\_time\_stamp\] \[--verbose\] \[--no\_cleanup\] \[--tree\_builder TREE\_BUILDER\] \[--iterations ITERATIONS\] \[--min\_snps MIN\_SNPS\] \[--filter\_percentage FILTER\_PERCENTAGE\] \[--prefix PREFIX\] \[--threads THREADS\] \[--converge\_method CONVERGE\_METHOD\] \[--version\] \[--min\_window\_size MIN\_WINDOW\_SIZE\] \[--max\_window\_size MAX\_WINDOW\_SIZE\] alignment\_filename

## DESCRIPTION

Gubbins supports rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.

Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.

## OPTIONS

### positional arguments:

- alignment\_filename

  Multifasta alignment file

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **--outgroup** OUTGROUP, **-o** OUTGROUP

  Outgroup name for rerooting. A list of comma separated names can be used if they form a clade

- **--starting\_tree** STARTING\_TREE, **-s** STARTING\_TREE

  Starting tree

- **--use\_time\_stamp**, **-u**

  Use a time stamp in file names

- **--verbose**, **-v**

  Turn on debugging

- **--no\_cleanup**, **-n**

  Don't cleanup intermediate files

- **--tree\_builder** TREE\_BUILDER, **-t** TREE\_BUILDER

  Application to use for tree building \[raxml\|fasttree\|hybrid\], default RAxML

- **--iterations** ITERATIONS, **-i** ITERATIONS

  Maximum No. of iterations, default is 5

- **--min\_snps** MIN\_SNPS, **-m** MIN\_SNPS

  Min SNPs to identify a recombination block, default is 3

- **--filter\_percentage** FILTER\_PERCENTAGE, **-f** FILTER\_PERCENTAGE

  Filter out taxa with more than this percentage of gaps, default is 25

- **--prefix** PREFIX, **-p** PREFIX

  Add a prefix to the final output filenames

- **--threads** THREADS, **-c** THREADS

  Number of threads to run with RAXML, but only if a PTHREADS version is available

- **--converge\_method** CONVERGE\_METHOD, **-z** CONVERGE\_METHOD

  Criteria to use to know when to halt iterations \[weigh ted\_robinson\_foulds\|robinson\_foulds\|recombination\]

- **--version**

  show program's version number and exit

- **--min\_window\_size** MIN\_WINDOW\_SIZE, **-a** MIN\_WINDOW\_SIZE

  Minimum window size, default 100

- **--max\_window\_size** MAX\_WINDOW\_SIZE, **-b** MAX\_WINDOW\_SIZE

  Maximum window size, default 10000

## SEE ALSO

Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley S. D., Parkhill J., Harris S.R. "Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins". Nucleic Acids Res. 2015 Feb 18;43(3):e15. doi: 10.1093/nar/gku1196.

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.