A software module for Multilocus Sequence Typing (MLST). MLST is a portable and precise state-of-the-art technique for typing bacteria and yeast isolates.

The MLST module is based on DNA sequence data from a number of house-keeping genes. For each gene, the experimental data is compared to a database of known alleles and a final sequence type is assigned by combining information from all genes.

CLC MLST Module integrates the MLST procedure into one single step. Simply select the sequencing data for all the loci, choose an MLST scheme, and a few seconds later you have a sequence type. You can easily inspect and edit the sequencing data to correct sequencing errors and verify the result. The MLST schemes can be downloaded from PubMLST, which also includes schemes from databases, and you can add new types to the scheme yourself.

With its graphical user interface CLC MLST Module is easy and intuitive to use. Advanced computer skills are not required, and the comprehensive user manual explains all the details.

Time saving
A typical MLST workflow includes assembly, inspection of assembly, trimming of sequence ends, copying and pasting into a web form, and noting the allele number. This tiresome routine must be repeated for all loci. Our usability studies show that this on average takes 25 minutes. With CLC MLST Module the workflow is concluded in less than a minute and with only a few clicks of the mouse, leaving less room for manual error and more time for inspection and verification of the results.

Supports iterative workflow
If your sequencing experiment fails for one or more loci, you can assign a preliminary sequence type based only on the successful experiments. After resequencing, data from the missing loci can be added to obtain the precise sequence type. In this way, data-driven corrections and adjustments can be made at any step in the typing process and no work is ever lost.

Saving results
Web-based MLST analysis leaves you no options to save and correct typing analyses, making it tiresome and difficult to repeat or adjust previous analyses. With CLC MLST Module you can easily save all your work and with a single click go back to review and adjust the results. Together with the history view, which records all the editing you make, this makes it easy to document, repeat, and refine your analyses.

Extend and develop your own schemes
CLC MLST Module makes it easy to download existing MLST schemes from any web site compatible with mlstDBnet, e.g. PubMLST ,, or University College Cork. After download, the user is free to customize the scheme by adding newly discovered, or proprietary, allele types. The MLST schemes can be merged, which makes it possible to update your own schemes with new types. Merging schemes also enables sharing of data among several users. Furthermore, you can easily create your own schemes if you work on an organism not represented in publicly available MLST schemes.

Integrated solution
CLC MLST Module is a seamlessly integrated plugin to CLC Main Workbench and CLC Genomics Workbench. This means that you get the benefit of a fully integrated bioinformatics solution for all your sequence analysis work with direct access to e.g. phylogeny, primer design, BLAST, SNP annotation, and virtual cloning.


Feature overview

  • Automatic assignment of sequences to loci
  • Automatic determination of allele number and sequence type
  • Add and remove isolate data
  • Inspect and edit sequencing data (contigs)
  • Automatic re-assignment of allele number and sequence type when editing is done
  • Download MLST schemes from PubMLST ,, or University College Cork
  • Easily extract and concatenate alignments and sequences for MultiLocus Sequence Analysis (MLSA)
  • Create custom MLST schemes
  • Merge and extend MLST schemes
  • Easily create isolate report with typing result
  • Elaborate history log to document changes and procedure

Version 1.0 for Windows, Mac OS X, and Linux



Plugin Manual

Download manual

Plugin Downloads

Download plugin

Download CLC MLST Module


Platform support



CLC Genomics Workbench

 [9.5.2, 9.5.1, 9.5, 9.0.1, 9.0]

CLC Main Workbench

 [7.7.3, 7.7.2, 7.7.1, 7.7]


CLC Genomics Workbench

 [8.5.3, 8.5.2, 8.5.1, 8.5, 8.0.3, 8.0.2, 8.0.1, 8.0]

CLC Main Workbench

 [7.6.6, 7.6.5, 7.6.4, 7.6.3, 7.6.2, 7.6.1, 7.6]


CLC Genomics Workbench

 [7.5.5, 7.5.4, 7.5.3, 7.5.2, 7.5.1, 7.5]

CLC Main Workbench

 [7.5.3, 7.5.2, 7.5.1, 7.5]


CLC Genomics Workbench

 [7.0.4, 7.0.3, 7.0.2, 7.0.1, 7.0]

CLC Main Workbench

 [7.0.3, 7.0.2, 7.0.1, 7.0]


CLC Genomics Workbench

 [6.5.2, 6.5.1, 6.5]

CLC Main Workbench

 [6.9.2, 6.9.1, 6.9]

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