Category Archives: howto

Geographical Heat Maps in R

I go crazy for fancy data visualizations in R, and a figure in a recent publication has had me wondering if there is an easy way to incorporate density distributions (or as in their case, a distribution of f4 statistics, … Continue reading

Posted in bioinformatics, howto, R, software | Tagged , | 2 Comments

Quick and dirty tree building in R

One of the major obstacles to turning your sequence data into phylogenetic trees is choosing (and learning) a tree-building program. Confounding this problem is the fact that most researchers will want to perform numerous, complementary analyses, each of which may … Continue reading

Posted in howto, methods, phylogenetics, R, software | Tagged , , , , , , , | 3 Comments

2D Posterior Density Plots in R

I have been grappling with visualizing two dimensional histograms of posterior density distributions of parameters, as estimated by one of your favorite programs – IMa2, MIGRATE-n, MSVAR, etc. All these programs print out distributions of estimated parameters, and here’s a … Continue reading

Posted in bioinformatics, howto, population genetics, R, software | Tagged , , , | 1 Comment

On false positives in Isolation with Migration analyses

The IM suite of tools (IM, IMa, IMa2, IMa2p, etc.) are used widely by molecular ecologists at large for the analyses and estimation of ancestral demography under an Isolation with Migration (IM) model. However, these tools come with fundamental assumptions … Continue reading

Posted in evolution, genomics, howto, IMa2, methods, Molecular Ecology views, natural history, population genetics, software, theory | Tagged , , , , , , , | 1 Comment

PCA of multilocus genotypes in R

An earlier post from Mark Christie showed up on my feed on calculating allele frequencies from genotypic data in R, and I wanted to put together a quick tutorial on making PCA (Principal Components Analysis) plots using genotypes. I used … Continue reading

Posted in bioinformatics, genomics, howto, population genetics, R, software | Tagged , , | 6 Comments

What do with all those pesky mtDNA reads in your NGS experiment

Have you ever noticed how many reads from your high throughput sequencing project map to the tiny fraction of your genome that is the mitochondrial genome (mtDNA)? Pretty much any NGS experiment (e.g., RNA-seq, DNA-seq, capture-based sequencing) leave you with … Continue reading

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IMa2p – Parallel Isolation with Migration Analyses

I figured that it was time to write an update on my post from a year ago on Bayesian MCMC in inferring ancestral demography. Recently, my postdoctoral advisor, Jody Hey and I released a version of the popular IMa2 program, … Continue reading

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marmap

A couple years ago, Benoit Simon-Bouhet ended up sharing an office with Eric Pante, then a post-doc fellow in his former lab. The two quickly realized they were in a lab in which few people had the expertise or taste for coding. Thus, on … Continue reading

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IBE/IBD Contour plots in R

Rob’s post from yesterday motivated me to find an alternate way of visualizing correlations between matrices of geographical or ecological data, and genetic data. I have seen plenty of Mantel, or partial Mantel tests of correlation, as well as plots … Continue reading

Posted in bioinformatics, howto, population genetics, R, software | Tagged , , , | 5 Comments

Procrustes Analyses in R

Procrustes transformations (i.e. a form of multidimensional scaling that allows the comparison of two data sets) have been used extensively in recent literature to assess the similarity of geographical and genetic distributions of species, following the lead of Wang et … Continue reading

Posted in genomics, howto, population genetics, R, software | Tagged , , , | 3 Comments