What’s new in MacSyFinder v2?

For Version 2, MacSyFinder was carried under Python 3.

New features and search engine

MacSyFinder v2 is a major release. The search engine was changed for a more intuitive and comprehensive exploration of putative systems.

The search is now more thorough and avoid undesirable side-effects of the previous search engine. Being more thorough, it now also includes a scoring scheme to build candidate systems from sets of detected components (clusters), and can offer several optimal “solutions” (sets of detected systems) based on a combinatorial exploration of detected clusters. See here for more details.


The search engine being different, one might want to check that models carried from v1 to v2 have the expected behaviour.

Several new features were added, including:

  • a new type of gene component “neutral” was added in order to provide more possibilities for systems’ modelling in macsy-models. See here for more details.
  • a new component feature was introduced: “multi-model”, that corresponds to components that are allowed to participate in occurrences of systems from different models. See here for more.
  • more flexibility was introduced in the search for systems’ components using HMMER. It is now possible to use the cut_ga threshold when provided in the HMM profiles used for components’ similarity search. This enables to have a search tailored for each HMM profile, and thus component. See here for more details.
  • a new file structure was created to better organize MacSyFinder’s packages (i.e. that include systems’ models and corresponding HMMER profiles). See here for details.
  • a tool to easily install and distribute MacSyFinder’s packages was created. See here for more details on macsydata.
  • the format for MacSyFinder’s models has slightly changed, in order to offer more possibilities, and more readibility. To see how to carry models from v1 to v2, visit here.

Also, the search modes corresponding to “unordered” and “unordered_replicon” were merged into the “unordered” search mode - as they basically correspond to the same behaviour.


In v2, output files were also re-defined. See here for more details.


MacSyFinder v2 no longer requires the formatdb or makeblastdb tools from NCBI. However, new dependencies are used, but as they are Python libraries, it should be transparent for the user, and not require manual installations. See here for details.

Models are more formalized

The models data are more formalized, with a well defined structure. For instance the definitions and profiles must be packed together in what we call a macsy-model package If you intend to model new systems please refer to the Modeller Guide.

Models installation

We now provide a new tool to manage the models. See Models installation with macsydata.

Models configuration

The modeler can provide some spcific configuration values released along the model package. See Model configuration.

Modeller helper tool

To help modellers create new models we provide a new helper tool macsyprofile, which analyses HMMER raw output files from results of a previous MacSyFinder run, to provide information on all hits even if filtered out. See macsyprofile.

Models installation with macsydata provide also some options to help the modeller as

  • macsydata init to init a new model package.
  • macsydata check to check the integrity of a model package, before to use/publish it.