Plant Secondary Metabolite Analysis
home download help about contact
Server status: unknown
Running jobs: unknown
Queue length: unknown
Oldest job in queue submitted
Long runtime queue: unknown
Oldest job in queue submitted
Jobs processed: unknown

Download plantiSMASH standalone

Stand-alone versions of plantiSMASH 1.0.beta are available through Bitbucket.

The current standalone release is plantiSMASH 1.0.beta (October 10th, 2016)

Please select the tab under "Source" for the guidance on manual installation through git. Under "extras", you can find some scripts that can aid in using plantiSMASH

Install from source

First of all, clone the plantiSMASH python source from our Bitbucket repo:
git clone

Then, make sure you have the following plantiSMASH dependencies installed:

  • glimmer (version 3.02 tested)
  • GlimmerHMM (version 3.0.4 tested)
  • hmmer2 (version 2.3.2 tested, append a 2 to all hmmer2 executables to avoid conflict with hmmer3 executable names, like hmmalign -> hmmalign2)
  • hmmer3 (version 3.0 and 3.1b2 tested)
  • fasttree (version 2.1.7 tested)
  • diamond (> 0.7.9 required, version 0.7.10 tested1)
  • muscle (version 3.8.31 tested)
  • prodigal (version 2.6.1 tested)
  • NCBI blast+ (version 2.2.31 tested)
  • CD-HIT (version 4.6.6 tested)
  • xz development headers (version 5.1.1 tested)
  • xml development headers (version 2.9.1 tested)
  • python (version 2.7 tested, anything >= python 2.6 should work)
  • python-virtualenv (not needed, but highly recommended)

Then, create a python virtualenv for installing the plantiSMASH python dependencies. This is not required, but highly recommended.

virtualenv as3source as3/bin/activate

All the python dependencies are listed in requirements.txt, you can grab them all and install them with a simple command:

pip install -r requirements.txt

Last but not least, run to grab and prepare the databases:


Scripts that can aid in using antiSMASH:

pHMM seed alignments
Seed alignments used for building pHMMs used in secondary metabolite cluster finding
analysis plug-in
Template code for creating your own antismash 2.0 analysis plug-ins
output plug-in
Template code for creating your own antismash 2.0 output plug-ins
Script for preparing an EMBL file from a TXT file with gene annotations and a DNA sequence in FASTA format
Script for batch-processing multiple files in antiSMASH version 1.x