Below is a list of software useful and appropriate for study with MLST data.
Included is a description of the software and links to the downloadable files

  Sequence Output by Nick Ross and Brian Spratt

Sequence Output is a simple Macintosh program that allows a set of sequences (in MEGA format) to be grouped into those that are identical (i.e. allele assignment), and allows all alleles to be compared to any selected 'master' allele, to identify the variable sites.

More information

Platform(s) - Windows DOS exe.



 MEGA by Sudhir Kumar, Koichiro Tamura, Ingrid Jakobsen and Masatoshi Nei  

The scope of computational molecular evolutionary genetics has expanded greatly with unparalleled growth of gene sequence databases in recent years. Efficient handling and analysis of these data for molecular evolutionary analysis require the development of easy-to-use computer programs. Therefore, the goal of the MEGA (Molecular Evolutionary Genetics Analysis) software project has been to make useful methods of comparative sequence analysis easily accessible to the scientific community for research and education.



Platform(s) - Macintosh, Sun WorkStation and Windows.



PAUP by David Swofford  
  PAUP* version 4.0 is a major upgrade and new release of the software package for inference of evolutionary trees.

The influence of high-speed computer analysis of molecular, morphological and/or behavioral data to infer phylogenetic relationships has expanded well beyond its central role in evolutionary biology, now encompassing applications in areas as diverse as conservation biology, ecology, and forensic studies.

The success of previous versions of PAUP: Phylogenetic Analysis Using Parsimony has made it the most widely used software package for the inference of evolutionary trees. In addition, the PAUP manual has proven to be an essential guide, serving as a comprehensive introduction to phylogenetic analysis for beginning researchers, as well as an important reference for experts in the field.

Platform(s) - Windows, UNIX/VMS, or DOS-based formats.

  Purchase - Website


Phylip by Joe Felsenstein  
  Phylip includes programs to carry out parsimony, distance matrix methods, maximum likelihood, and other methods on a variety of types of data, including DNA and RNA sequences, protein sequences, restriction sites, 0/1 discrete characters data, gene frequencies, continuous characters and distance matrices.
It is the most widely-distributed phylogeny package, with over 7,000 registered users, some of them satisfied. It competes with PAUP* to be the program responsible for the most published trees.

It has been distributed since October, 1980. .
Platform(s) - pre-386 DOS, 386/486/Pentium DOS, Windows 3.1, Windows95/98/NT, 68k Macintosh, or PowerMac.

  Download - Website

START by Keith Jolley  
The purpose of this program is to bring together some of the analyses which can be performed on MLST data into a single package. Written for Windows.

Platform(s) - Windows95/98/NT

  Download - Website