Working notes for Goteborg, 2011

Programming notes: algorithms, implementation, about BEAST and programming tools, etc

2011-04-11. Understanding BEAST. My documentation for the parts of BEAST and *BEAST that interest me.

2011-05-20. My implementation. Documentation for my code as it develops.

2011-06-21. My implementation - update. Documentation for my code as it develops.

2011-07-14. My implementation - update. Documentation for my code as it develops.

2011-08-31. My implementation - update. This is a description of my code when I committed it to the BEAST repository for the first time, 2011-09-01.

2011-09-08. Simulation program. R code 'AlloppSim', Andrew Rambaut's Seq-Gen, for diploids and allotetraploids.

2011-09-15. My implementation - update. Documentation for my code as it develops. This is for the model AlloppNET for two diploids and one hybridization. See 2012-01-09 for AlloppMUL.

2011-09-19. SVN, Java, Linux. Notes on Java, Eclipse, TortoiseSVN, Linux. CLASSPATH, -enableassertions, etc.

2011-10-11. Plans for simulations. Organization of directory structure and file names. Method of choosing random seeds.

2011-10-21. SVN, Java, Linux, Albiorix. Update of 2011-09-19 PDF. Notes on TortoiseSVN; Java and Eclipse; R, Eclipse, BEAST and AlloppSim on Ubuntu (netbook); and similar on Albiorix plus sftp, ssh.

2011-10-21. Simulation program AlloppSim. Mostly an update of 2011-09-08-simulations.pdf. R code 'AlloppSim', Andrew Rambaut's Seq-Gen, for diploids and allotetraploids. Now does a complete set of simulations and runs BEAST on them.

Other notes: theory, simulation results, user manual, draft article

2011-04-09. Probability distributions for MUL-trees. Tentative discussion with Serik.

2011-09-17. Network prior. Discussion of network prior. Birth-death process for homoploid subtrees, plus hybridization events, plus legs as an 'afterthought'.

2011-09-22. On hybridization rates. A rough calculation of likely hybridization rates, and particularly allopolyploidization rates, based on a simple model and observed rates of polyploidy.

2011-09-23. Simple population model. A simpler model than *BEAST uses for population sizes in a setting like *BEAST or allopolyploid networks. Each branch has a constant populaton which is drawn independently from a prior.

2011-10-17. First results from simulations. Preliminary results for three scenarios with two diploids and one tetraploid. G=1,3,10, N=1,3, two mutation rates.

2011-10-25. Notes on PADRE algorithm.

2011-10-31. Prior on MUL trees. Some calculations and simulations to help understand what it means for numbers of hybridizations if a prior such as the Yule prior is used for MUL trees.

2011-11-06. Yule densities This is working out the normalization factors for the density of nodes times and labelled histories (like Gernhard). It might be useful for network priors.

2011-11-07. On network prior. An idea for a network prior which didn't work.

2011-11-23. Program for network prior. Description of a program for investigating network priors empirically.

2011-11-30 Draft article for case of one hybridization. Assumes a single hybridization. Includes simulation results.


2011-09-26. AlloppSim (1st version). ZIP file containing Simulation program. See PDF at 2011-09-08.

2011-10-21. AlloppSim (2nd version). ZIP file containing simulation AlloppSim in R and Seq-Gen source code. See See PDF at 2011-10-21.