Plant Secondary Metabolite Analysis
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Download plantiSMASH standalone

Stand-alone versions of plantiSMASH are available through our GitHub page.

The current standalone release is plantiSMASH 1.0 (December 12th, 2019).

Install from source

First of all, download the plantiSMASH python source from our GitHub repo:

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