Sequence Clustering with Interpolated Markov Models (Kelley and Salzberg, 2010).
The plugins takes as input a TXT file of keyword-value pairs, whitespace-delimited: inputfile: FASTA file of sequences numclusters: Number of clusters
The plugin will output a TXT file mapping every sequence label to a cluster number (0 to numclusters-1).
This plugin includes some files from the SCIMM software package, available open-source on the following site: http://www.cbcb.umd.edu/software/scimm/
SCIMM is available under the Artistic License, available under scimm/LICENSE.
SCIMM source files have been slightly modified, summarized by two main changes:
- Removed generation of tmp folders
- Added an "outfile" parameter
HMP_MOCK sequence set was taken from the MiSeqSop pipeline (Kozich et al, 2013).