Software

• DualBrothers: implements dual multiple change point model that infers number and location of evolutionary change points and topology change points separately.
• cbrother: C version of above plus implements prior to test whether two recombinants with identical mosaic structure descend from one or more recombination events. A more up-to-date (non-public release) version is available cbrother1.4.tar.gz

Manuscripts

• Minin, Dorman, Suchard (JSM)
• Fang, Suchard, Rischmiller, Dorman (In progress)
• Minin, Dorman, Fang, Suchard (Bioinformatics)
• Ashlock, Schonfeld (CEC)

Ideas

• Suchard (2005-05-17): MrBayes finds 30% increase in speed using float instead of double. RESULTED IN 16% SPEED INCREASE IN CBROTHER!
• Dorman (2005-05-17): The trouble with Al-Awadhi and relaxing parental tree txt
• Dorman (2005-05-14): Thoughts on molecular clock and Keith05 and polyphyletic regions txt
• Dorman (2004-09): Thoughts on molecular clock txt
• Suchard (2004-09): Molecular clock model of recombination pdf.

Data

• HIV data set AH-AZ: A collection of thousands of directories, each containing a pending compute job. The files in this directory are:
  • job.txt: information about the job (configured for a XGrid). In particular see the line that starts with "job command" for the command to run.
  • [acn]t.phy: where [acn] is an accession number identifying the job. This is the PHYLIP-formatted alignment file.
  • [acn].cmdfile: this is an auxiliary file needed to run the command.
• Corrections to HIV data set AH-AZ: about 6,000 of the 40,000 jobs in the original file had incorrect cmdfiles. This smaller file contains corrected versions of those 6,000 files. The bad jobs are distributed throughout the directories AY1 through AY9.

Progress Reports

• Progress report 2005
• Progress report 2004

Bibliography

• Magiorkinis (2003): the paper showing recombination is associated with sequence conservation that Robertson recently criticized (Carpenter)
• Wolff (2003): a paper about identifying INS (inhibitory sequence) elements in HIV, a non-coding RNA motif previously known to exist but uncharacterized (Carpenter)
• Strimmer01a: ARG (Ancestral Recombination Graph) for recombination is an example of a molecular clock model with recombination
• Strimmer00: DAG for recombination (background for Strimmer01a)
• Keith05: Gibbs tree sampler
• Holmes04: RNA secondary structure evolutionary model
• There have been others...