SSuMMo is a library of functions designed around iteratively using hmmer to assign sequences to taxa. Results are highly annotated trees showing species / genus distribution within that community.
Programs included with the source code include tools to:-
- Build a hierarchical database of hidden Markov Models - dictify.py;
- allocate sequences to recognised taxonomic names - SSUMMO.py;
- analyse biological diversity, using Simpson, Shannon & other methods- rankAbundance.py;
- visualise results as cladograms with a distinct ability to easily cross-compare datasets - comparative_results.py
- convert results to phyloxml format: dict_to_phyloxml.py ;
- build html representation - dict_to_html.py .
- plot rarefaction curves and calculate corresponding biodiversity indices
Python source code is provided here, on google code. The prebuilt hierarchical database of HMMs, as well as an optimised SQL taxonomy database (used for deducing ranks of each taxon) can be downloaded from:- http://bioltfws1.york.ac.uk/ssummo/Download/
For install information, please refer to the README. For usage information, there is a wiki (above), and a preliminary User Manual has been added to the svn trunk.