Are We There Yet it is a simple web application to explore graphically convergence in Markov Chain Monte Carlo in Bayesian phylogenetic inference. The website name comes from one of the most important factors in Bayesian phylogenetic inference, that is the convergence of branch lengths and splits. Usually a linear plot of likelihood scores is ... Read more »
J Nylander, J C Wilgenbusch, D L Warren, & D L Swofford. (2007) AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics, 24(4), 581-583. DOI: 10.1093/bioinformatics/btm388
tested on a Pentium 4, 3 Ghz running Fedora Core 8
David Posada released sometime ago jModelTest, a program that tries to be the ultimate maximum likelihood model selector for phylogenies. Written in Java, jModelTest is cross-platform, but differently from the latest available Java-based programs that are executables, the program is distributed as a jar file. ... Read more »
This is a new series here at the Blind.Scientist headquarters. My team and I will try to feature one scientific publication a week, it might not be hot from the presses or it might not be only about biology and/or bioinformatics. We (my team and I) will try to be eclectic and cover different areas. [...]... Read more »
Noble, W. (2009) A Quick Guide to Organizing Computational Biology Projects. PLoS Computational Biology, 5(7). DOI: 10.1371/journal.pcbi.1000424
The paper of this week touches a subject that I have been involved in the past: sequence simulation. INDELible, by Fletcher and Yang, is a program that is capable of simulating both DNA and amino acid sequences, and it seems to be the complete package to do so. It contains several substitution models and it [...]... Read more »
Fletcher, W., & Yang, Z. (2009) INDELible: A Flexible Simulator of Biological Sequence Evolution. Molecular Biology and Evolution, 26(8), 1879-1888. DOI: 10.1093/molbev/msp098
Image by Getty Images via @daylife I cannot wait until all the omics for all bodily fluids are uncovered: “Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base” Ai, J., Smith, B., & Wong, D. (2010). Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base BMC Bioinformatics, 11 (1) DOI: 10.1186/1471-2105-11-302... Read more »
Ai, J., Smith, B., & Wong, D. (2010) Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base. BMC Bioinformatics, 11(1), 302. DOI: 10.1186/1471-2105-11-302
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