|
|
-
April 2005
A pre-alpha version of the graphical user interface for X11, using the GTK toolkit has been made avilable
with the source download. Use the gtk-build.sh script, which assumes that GTK+ 2.2.4 or later is installed on your system. Please use our
Bugzilla to leave your comments/suggestions.
-
January 2005
HyPhy application note has been published (at last)
Sergei L. Kosakovsky Pond , Simon D. W. Frost , and Spencer V. Muse HyPhy: hypothesis testing using phylogenies
Bioinformatics Advance Access published on October 27, 2004, DOI 10.1093/bioinformatics/bti079.
-
January 2004 - Nobody ever releases software on time, now do they? Version 0.99 is coming along, but distractions abound. In the meantime, check out the new HyPhy Guide available from http://www.hyphy.org/docs/hyphydoc.tgz , and http://www.datamonkey.org/ - a web based interface for detecting adaptive and purifying selection in sequences and model selection.
- November 2003 - while we are working to verify the stability of the 0.99 release and writing some documentation, you can check out the recent builds of HyPhy at http://www.hyphy.org/current/index.php
Some of the new features:
- A whole new suite of positive selection tools, including a very quick non-parameteric method derived from Suzuki-Gojobori and an approximate site by site likelihood selection detection. Both methods are much faster than full likelihood (counting methods can run 100 sequence alignments on a modern desktop in 5-10 minutes), and provide statistical significance for every site identified as positively and negatively selected. Details of methods will be published in an upcoming paper by Kosakovsky Pond and Frost. Methods can be run in parallel on MPI clusters and have been used to analyze datasets with hundreds of sequences.
- The abilility to rigorously compare and contrast selective pressure between populations/genes.
- HyPhy has been thourougly updated to take advantage of clusters. Most standard analyses transparently utilize distributed nodes when appropriate. Also, some single large analyses (most notably with rate variation), can run in parallel on clusters.
- Numerous interface improvements and enhancements. A number of new tree comparison tools, sequence search, filtering tools. Exact Fisher tests for association on sequence data.
- Many new features in the batch language to enable sequence data processing.
- Much improved distance and likelihood phylogenetic tools, including constrained topology searches.
- A collection of interface and batch language commands to determine parameter estimate errors, by a variety of methods.
- Aminoacid fitness models of Goldman and Dimmic, to look for functional constraints (and their variation along the sequence) in protein coding data.
- Speed and stability enhancements.
- September 2003 - we are working on preparing a 0.99 release of HyPhy with a host of bug fixes, new analyses, interface enhancements and MPI support. Hopefully, the release will occur before the end of November.
| |
|
Sergei L. Kosakovsky Pond, Spencer V. Muse and Simon D.W. Frost, Last modified: January 27, 2004, at 04:44 PM.
| 