Blog Grid

Analyzing ddRADseq Data in SNAPP

Oh, SNAPP… Over the last year, as I’ve become increasingly comfortable with GitHub, I’ve naturally shifted all of my note writing to Markdown language. During the process, I’ve started frequently jotting down useful notes related to analysis, code, or scientific computing as “Gists” on GitHub. In contrast to most repositories, Gists are small snippets of code […]

Converting scientific manuscripts from Word to LaTeX PDF on Mac

LaTeX is a very powerful document preparation and typesetting system that provides an accessible means for the programming-minded user to prepare beautiful scientific documents of all kinds, including manuscripts, software documentation, theses and dissertations, etc. Because documents typeset in LaTeX exhibit a high degree of professionalism in their design, while also rendering computer- and math-related […]

Running AMOVA (analysis of molecular variance) on biallelic SNP data in R

AMOVA in R Resources for conducting population genetic and phylogenetic analyses in the R computing environment are continually improving, and to date several packages have provided functions for estimating phi-statistics and hierarchical patterns of population variance partitioning using AMOVA (analysis of molecular variance; Quattro et al. 1992). The paper for the AMOVA method, penned by […]

Data mining resources for species distribution modeling and macroecology

Research projects in ecology, evolution, and conservation biology increasingly rely upon ecological modeling and GIS data and tools for manipulating and analyzing spatially linked data from across a variety of spatial scales. Of particular importance are species distribution modeling (SDM; also known as Ecological Niche Models, or ENMs, or Environmental Niche Models) and niche divergence tools, […]

Setting DNA substitution models in BEAST

BEAST (Bayesian Evolutionary Analysis Sampling Trees) software provides a growing set of clear options for specifying evolutionary models of DNA substitution for alignments loaded into the program. However, the set of models that are readily available and “spelled out” in drop-down menus in the BEAUti (Bayesian Evolutionary Analysis Utility) GUI is much smaller compared to […]

Latest *BEAST trace: Most beautiful thing I’ve seen today

My new *BEAST (starbeast) species tree runs are converging wonderfully in BEAST v1.8.3, so I am off to a great start this morning. Here, I’m including a screenshot of the results of one of these runs, which I ran for 200 million generations using 3 normally distributed calibration points, as visualized in Tracer. Note the good posterior trace, very high ESS […]