kclust - Perform fast and sensitive clustering¶

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

Uses kClust to generate clusters of amino acid sequences.

Parameters:	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.
Returns:	A list of cluster instances
Raises:	FileNotFound if kClust could not be located.

class cluster(sequences, representative_id)¶

Holds the information of one cluster

sequences¶

SequenceList containing all sequences of the cluster

representative_id¶

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

alignment¶

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