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.
- SplitsTree
- 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.
- LIAN - Linkage analysis
- LIAN is a program to test the null hypothesis of linkage equilibrium for multilocus data. The 'standardised' Index of Association (IA) generated by LIAN should be used in preference to the classical IA of Maynard-Smith as the latter scales with the number of loci analysed.
- LIAN was written by Bernhard Haubold and Richard Hudson and is described in Haubold & Hudson 2000, Bioinformatics 16:847-849.
- Shustring
- Shustring is a program for Computing SHortest Unique SubSTRINGs
- Shustring was written by Bernhard Haubold and Thomas Wiehe and is described in Haubold et al. 2005, BMC Bioinformatics 6:123.
- BURST
- BURST is a clustering algorithm designed for use with MLST data. The algorithm was developed by Ed Feil.
- This is the original BURST implementation written by Man-Suen Chan.
- Tree drawing
- This tool uses the PHYLIP suite of programs to generate neighbor-joining and UPGMA trees from allelic profile data. Tree display and output (in gif, pdf, pict, or ps formats) is performed using Phylodendron.
- Minimum-spanning tree
- This tool uses Prim's algorithm to draw a minimum-spanning tree from MLST profile data.