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This blog gravitates around statistical methods for evolutionary studies, which means you can expect to see a lot of Bayesian statistics, non-Bayesian statistics, phylogenetics, molecular evolution and the algorithms that glue them together. We can eventually talk about philosophy of science, virology or gastronomy – from a probabilistic point of view, of course…

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  • October 10, 2014
  • 11:54 AM

A "parsimonious" Bayesian supertree model for estimating species trees

by Leonardo Martins in bioMCMC

When we have sequence alignments regarding several genes from a group of taxa, we usually want to extract the phylogenetic information common to all of them. However, in many cases such phylogenomic analyses depend on selecting one sequence from each species per gene family (=alignment), or excluding paralogs, or partitioning these paralogous sequences into loci, or utilizing only gene families without apparent paralogs. If we want to analyse all our data at once, without excluding sequences or ........ Read more »

  • February 7, 2013
  • 06:07 PM

The difference between the RF and the NNI distance

by Leonardo Martins in bioMCMC

Just to complement my answer to a blog post, where I maintain that the Nearest-Neighbor Interchange (NNI) distance is not equivalent to the Robinson-Foulds (RF) distance, a simple example:Where we can see that trees T1 and T2 differ only in the location of nodes A and B -- on these trees, we can naturally think of the nodes A, B, 1,..., 6 as representing leaves, but they might also be large subtrees.The RF distance is the number of edges (=branches) that are unique to each tree (that's why it's ........ Read more »

Bryant David. (2004) The Splits in the Neighborhood of a Tree. Annals of Combinatorics, 8(1), 1-11. DOI: 10.1007/s00026-004-0200-z  

  • May 15, 2012
  • 03:29 PM

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

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

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 »

  • May 16, 2010
  • 10:17 PM

fault-tolerant conversion between sequence alignments

by Leonardo Martins in bioMCMC

Despite I’m very charitable when testing my own programs, I’m not so nice when asked to scrutinize other people’s work. That’s why I was happy to see the announcement about the ALTER web server being published at Nucleic Acids Research (open access!). I am not involved in the project, but I was in the very [...]... Read more »

Glez-Pena, D., Gomez-Blanco, D., Reboiro-Jato, M., Fdez-Riverola, F., & Posada, D. (2010) ALTER: program-oriented conversion of DNA and protein alignments. Nucleic Acids Research. DOI: 10.1093/nar/gkq321  

  • April 27, 2010
  • 07:04 PM

The specialization of novel genes

by Leonardo Martins in bioMCMC

Recently a paper about the software MANTiS called my attention, and I’ve been trying to write about it for a while. This announcement at the EvolDir list seemed like the perfect opportunity. I must warn you though that I’ve never used the software and I don’t have any intimacy with the underlying databases, but the [...]... Read more »

Milinkovitch, M., Helaers, R., & Tzika, A. (2009) Historical Constraints on Vertebrate Genome Evolution. Genome Biology and Evolution, 13-18. DOI: 10.1093/gbe/evp052  

Tzika, A., Helaers, R., Van de Peer, Y., & Milinkovitch, M. (2007) MANTIS: a phylogenetic framework for multi-species genome comparisons. Bioinformatics, 24(2), 151-157. DOI: 10.1093/bioinformatics/btm567  

  • March 20, 2010
  • 11:10 PM

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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