Site-Specific Relative Evolutionary Rates · 2008-01-03 10:13 by Andrew Fernandes
Given a multiple sequence alignment, a phylogenetic tree, and an evolutionary model, this program calculates site-specific relative evolutionary rates.
A detailed manuscript describing its theory, implementation, and testing has been published in Oxford’s Bioinformatics (PubMed 18662926)
Note: there is a missing sentence in the Methods section of the original version of the article linked above! Silly me, but I accidentally left off a sentence giving the Hastings-ratio of my Metropolis-Hastings Markov chain Monte Carlo procedure to sample the unit-simplex. The correct procedure can be found on the entry I added to wikipedia on performing a random-walk on the simplex.
- Version 35 (16 February 2009)
- bRate-r35.tgz [415.66KB]
- Minor bugfixes in the likelihood engine
- Included a tool to create your own substitution matrices
- Includes all the matrices from PAML 4.2a
- Added a hack to increase numeric stability on long MCMC runs
- Completely verified the likelihood engine against PHYML 3.0
- The only thing we don’t do is tree rearrangements
- I’ll probably still twiddle with the rate-proposal function
- Something is odd about the summarized “expected rate” value. It is correctly calculated (carefully verified) but it gives a surprisingly high and anomalous likelihood. I’ll have to track this down.
- Version 25 (30 January 2009)
- Complete rewrite of the recursive likelihood engine
- Can now start the likelihood calculation from arbitrary tree nodes
- This will be useful later on when we compute probabalistic ancestors
- In the future we will compute marginals at each tree node
- New! We now integrate over all possible branch lengths, making bRate the first system to treat rates and branch lengths as completely identifiable!
- The last line printed upon quitting is the expected rates, branch lengths, and tree, averaged over the appropriate manifold (the geometric mean)
- Switched to CMake for the build system
- Version 19 (26 August 2008)
- Minor bugfixes in the likelihood code
- Version 18.38M (03 January 2008)
- Initial release
