This document is for OpenStructure version 1.6, the latest version is 2.7 !

kclust - Perform fast and sensitive clustering

kClust(sequences, clustering_thresh=30, create_alignments=False)

Uses kClust to generate clusters of amino acid sequences.

  • sequences (ost.seq.SequenceList) – All sequences you want to cluster.
  • clustering_thres – Sequence identity threshold to build clusters. Note, that clustering_thresh is more a rule of thumb, since compositional bias in the sequence can also play a role. The value gets transformed in a bitscore, that is used as an input parameter of kClust
  • create_alignments – Flag, wether the alignments of the clusters get calculated. Requires clustalw in the path.

A list of cluster instances


FileNotFound if kClust could not be located.

class cluster(sequences, representative_id)

Holds the information of one cluster


SequenceList containing all sequences of the cluster


a string, that contains the name of the representative sequence of the cluster as estimated by kClust.


alignment handle containing a multiple sequence alignment of all sequences of the cluster. Gets only calculated when binding is called with appropriate flag.


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Documentation is available for the following OpenStructure versions:

dev / 2.7 / 2.6 / 2.5 / 2.4 / 2.3.1 / 2.3 / 2.2 / 2.1 / 2.0 / 1.9 / 1.8 / 1.7.1 / 1.7 / (Currently viewing 1.6) / 1.5 / 1.4 / 1.3 / 1.2 / 1.11 / 1.10 / 1.1

This documentation is still under heavy development!
If something is missing or if you need the C++ API description in doxygen style, check our old documentation for further information.