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All posts; Tags Include "Bayesian Statistics"

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  • May 15, 2012
  • 03:29 PM
  • 798 views

Testing for common ancestry

by Leonardo Martins in bioMCMC

Our commentary on Douglas Theobald's test from Universal Common Ancestry (UCA) just went online. The original idea was to make a user-friendly review of his analysis described in "A formal test of the theory of universal common ancestry", but after a long e-mail exchange between Douglas and us -- actually between him and David, I didn't say much -- we decided to expand the article to include some remaining points of skepticism and spell out the basic problem with his approach.His work His test f........ Read more »

Leonardo de Oliveira Martins, David Posada. (2012) Proving universal common ancestry with similar sequences. Trends in Evolutionary Biology, 14(1). info:/10.4081/eb.2012.e5

  • August 6, 2011
  • 04:46 PM
  • 721 views

How to summarise a collection of trees that came from a Bayesian analysis

by Leonardo Martins in bioMCMC

After running a Bayesian phylogenetic analysis we are usually left with a large collection of trees, that came from the posterior distribution of the model given our data. Then if we want to work with a single tree - that is, to have a point estimate of this posterior distribution of trees - the most usual ways are to calculate the consensus tree or to select the most frequent tree. There are other ways, but let's fix on those by now.We might not be aware of it, but when we choose for one or ano........ Read more »

Huggins, P., Li, W., Haws, D., Friedrich, T., Liu, J., & Yoshida, R. (2011) Bayes Estimators for Phylogenetic Reconstruction. Systematic Biology, 60(4), 528-540. DOI: 10.1093/sysbio/syr021  

  • July 12, 2010
  • 06:09 PM
  • 1,683 views

Distribution of recombination distances between trees – poster at SMBE2010

by Leonardo Martins in bioMCMC

I just came back from SMBE2010, where I presented a poster about our recombination detection software and had the chance to see awesome research other people are doing. The poster can be downloaded here (1.MB in pdf format) and I’m distributing it under the Creative Commons License. Given the great feedback I got from other [...]... Read more »

  • March 20, 2010
  • 11:10 PM
  • 2,754 views

Using System-on-a-Chip hardware to speed up alignments

by Leonardo Martins in bioMCMC

In recent years there has been an explosion of parallel algorithms for solving bioinformatics problems, namely phylogenetic reconstruction and sequence alignment. These algorithms follow the growth of new hardware solutions like  Field-Programmable Gate Arrays (integrated circuits capable of  performing simple instructions in parallel), Cell microprocessors (like the one inside Playstation 3), Graphics Processing Units (nvidia [...]... Read more »

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