MLST Data Analysis
NB. This page can be cited and bookmarked as http://pubmlst.org/analysis/.
- Non-redundant databases (NRDB)
- NRDB can be used to compare batches of sequences to find those that are identical. This can be useful when developing new MLST schemes or where a database does not yet exist.
- The program was written by Warren Gish, Washington University.
- NRDB align
- This tool combines NRDB with EMBOSS showalign, taking a FASTA file of aligned sequences as input and displaying the distinct sequences in an interleaved format.
- NRDB was written by Warren Gish, Washington University.
- EMBOSS showalign was written by Gary Williams, MRC Rosalind Franklin Centre for Genomic Research, Wellcome Trust Genome Campus, Hinxton, UK.
- Use this tool to perform split decomposition analysis on allelic profile data using a web version of SplitsTree. The distance matrix can also be saved in NEXUS format and loaded into the stand-alone version of the software for more detailed analysis.
- SplitsTree was written by Daniel Huson. Further details can be found in Huson 1998, Bioinformatics 14:68-73.
- Tree drawing
- Minimum-spanning tree
- This tool uses Prim's algorithm to draw a minimum-spanning tree from MLST profile data.