The Dart Library: XRate, Handel, Stemloc, EvolDeeds & more...
For instructions on how to get dart, go to this page: Downloading dart.
For installation, go here: Building dart.
What is 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, etc.)
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 does DART run on?
works for sure on Linux and Mac OS X. It can probably be coaxed to build on anything with GNU make
? Possibly, e.g. with CygWin
adds (Dec. 17, 2007): just compiled DART
(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 do the individual programs do?
The various programs do a lot of different things including PhylogeneticAlignment
; 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...
Handel: evolutionary alignment & reconstruction with string transducers
allows MCMC sampling of multiple alignments, phylogenetic trees, evolutionary parameters & reconstructed indel/substitution histories.
- phylocomposer (link) - tests phylogenetic transducer composition and inference
XRate: alignment annotation & ancestral reconstruction with phylo-SCFGs
Annotating conserved features; measuring rates; reconstructing substitution histories.
- 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
Stemloc: RNA multiple alignment with pair-SCFGs
Secondary structure-aware RNA multiple alignment; reconstruction of indels and changes in structure.
- stemloc (link) - simultaneously
- align RNA sequences,
- predict secondary structure and
- infer evolutionary history
EvolDeeds: phylogenetic RNA alignment & reconstruction with tree transducers
- indiegram (link) - three-way RNA alignment and reconstruction using tree transducers and the TKF structure tree
Scripts and modules
What file formats does DART understand?
Standard file formats include
Dart-specific file formats include
Dart also has a detailed logfile
How can I download it?
See Downloading Dart
and Building Dart
for information on how to download and install the programs.
Who (else) uses it?
Average: 30 anonymous downloads per month in 2007.
Why doesn't X, Y or Z 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
(And there is an extra incentive to do this: see BoozeForBugs
What are the licensing terms?
Why is it called "dart"?
Originally named after a '66 Dodge Dart,
now a backronym
for DNA, Amino and RNA Tests
Whose fault is all this?
The code and most of the documentation pages are maintained by IanHolmes
Contributors of code to date include SeanEddy
, David MacKay
and contributors to RandLib
Testers include the contributors listed above, as well as RahulSatija
Contributors to the design include RichardDurbin
and many others in the evolutionary bioinformatics community.
How do I get help/information/etc?
How do I reference dart?
For papers describing the software and algorithms, see the PaperArchive