The Dart Library: XRate, Handel, Stemloc & more...

For instructions on how to get dart, go to this page: Downloading dart.

What it is?

The DART library includes a number of bioinformatics programs, including: stemloc for RNA alignment; xrate for phylo-grammars; phylocomposer and other statistical alignment programs in the Handel package; and more.

The programs use statistical algorithms (MCMC, EM) to impute multiple alignments, annotations and other unseen evolutionary parameters from sequence data. All are based on stochastic grammars or state-machine models of sequence mutation and natural selection.

Dart can be downloaded as a directory tree containing source files for the above programs, along with supporting code, tests, scripts and utilities.

What platforms it runs on?

DART works for sure on Linux and Mac OS X. It can probably be coaxed to build on anything with GNU make and gcc.

Microsoft Windows? Possibly, e.g. with Cyg Win. Untested.

Andrew Uzilov adds (Dec. 17, 2007): just compiled DART on cygwin (gcc 3.4.4, cygming special, gdc 0.12, using dmd 0.125) on Microsoft Windows XP Home Edition (SP2) on a Dell Inspiron 1000 (w/Intel Celeron) with no problems! Only tried xrate, but it runs as intended. The bundled Perl (e.g. windowlicker) works fine also.

What the programs do?

The various programs do a lot of different things including Phylogenetic Alignment; RNA structure prediction & multiple RNA alignment; stochastic grammars; evolutionary models, phylo-HMMs and phylo grammars; reconstruction of ancestral sequences; and phylogenomics.

Specific sub-packages address the following tasks...

Multiple alignment with string transducers

tkfalign

• tkfalign (link) - program for Phylogenetic Alignment
  • samples multiple alignments and phylogenies from the posterior probability distribution implied by the Thorne Kishino Felsenstein & other indel models

handalign

• handalign - in development: samples alignments and phylogenies using an affine gap string transducer

phylocomposer

• phylocomposer (link) - tests phylogenetic transducer composition and inference

Alignment annotation with phylo-grammars

xrate

• xrate (link) - estimate maximum likelihood substitution rate matrices by EM
  • xgram, xfold and xprot - analyze and annotate multiple alignments, phylogenetically, using evolutionary context-free grammars and EM

RNA multiple alignment with Pair SCFGs

stemloc

• stemloc (link) - simultaneously
  1. align RNA sequences,
  2. predict secondary structure and
  3. infer evolutionary history

evoldoer

• evoldoer (link) - experimental RNA alignment using tree transducers

Scripts

The Perl programs in dart/perl/ are described here: Dart Perl Scripts.

What file formats it speaks?

Standard file formats include

• Fasta Format for sequences
• Newick Format for trees
• Stockholm Format for alignments

Dart-specific file formats include

• XRate input format for phylo grammars
• Phylocomposer input format for string transducers

Dart also has a detailed logfile system.

How to download dart?

See Downloading Dart and Building Dart for information on how to download and install the programs.

Who (else) uses it?

• DART access statistics at Sourceforge
• DART paper archive (incomplete)

Average: 30 anonymous downloads per month in 2007.

Why X, Y or Z doesn't work?

Check the known issues with DART page for bug reports, anecdotal usage info, etc. Browse other pages on this wiki for documentation. If feeling bold, turn on logging which may give some insight into your problem.

If none of that helps, mail to Ian Holmes, preferably after checking the DART bug reporting guidelines. (And there is an extra incentive to do this: see Booze For Bugs.)

What the licensing terms are?

GPL.

Why it's called "dart"?

Originally named after a '66 Dodge (like this one), "dart" is a backronym for DNA, Amino and RNA Tests.

Whose fault this all is?

The code and most of the documentation pages are maintained by Ian Holmes.

Contributors of code to date include Sean Eddy, Graeme Mitchison, Robert Davies, Bill Bruno, Ian Holmes, David MacKay, Gerton Lunter, Pete Klosterman, Robert Bradley, Andrew Uzilov, Yuri Bendana, Sharon Chao, Kenny Duong, Andrew Uzilov, Avinash Varadarajan, Lars Barquist, Andreas Heger, Gabriel Wu and contributors to RandLib and LAPACK.

Testers include the contributors listed above, as well as Rahul Satija, Benedict Paten, Carolin Kosiol, Nick Goldman, Alex Bateman, Sam Griffiths Jones, Ryan Ritterson, Karsten Temme, Christopher Van Belle and others.

Contributors to the design include Richard Durbin, Ewan Birney, Guy Slater, David Haussler, Jotun Hein, Kevin Karplus, Gary Stormo, Chris Mungall and many others in the evolutionary bioinformatics community.

How to get help/information/etc?

• Dart Mailing Lists (dart-announce, dart-help)
• Dart Release Notes
• Known issues with DART
• Dart Bug Reporting

How to reference dart?

For papers describing the software and algorithms, see the Paper Archive.