5 posts · 3,031 views
science, bioinformatics, biology
nuin
5 posts
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- March 10, 2008
- 06:10 PM
- 862 views
Are we there yet? Pretty much.
by nuin in Blind.Scientist
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
- April 21, 2008
- 05:18 PM
- 647 views
jModelTest
by nuin in Blind.Scientist
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 »
D Posada. (2008) jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution. DOI: 10.1093/molbev/msn083
- August 3, 2009
- 08:11 PM
- 539 views
Paper of the week: A Quick Guide to Organizing Computational Biology Projects
by nuin in Blind.Scientist
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
- August 10, 2009
- 11:09 AM
- 521 views
Paper of the week: INDELible: A Flexible Simulator of Biological Sequence Evolution
by nuin in Blind.Scientist
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
- June 4, 2010
- 10:42 AM
- 462 views
Thank the Lord it’s Friday!
by nuin in Blind.Scientist
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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