Category Archives: howto

On false positives in Isolation with Migration analyses

Posted on 19 Oct, 2015 by Arun Sethuraman

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

Posted on 30 Jul, 2015 by Arun Sethuraman

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

Posted on 21 Jul, 2015 by Noah Snyder-Mackler

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 →

Posted in bioinformatics, genomics, howto, mutation, software, Uncategorized | Tagged , | Leave a comment

IMa2p – Parallel Isolation with Migration Analyses

Posted on 16 Jul, 2015 by Arun Sethuraman

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 →

Posted in bioinformatics, genomics, howto, software, theory | Tagged , , , , , | 1 Comment

marmap

Posted on 3 Jul, 2015 by Stacy Krueger-Hadfield

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 →

Posted in community ecology, conservation, evolution, howto, natural history, R, software | Tagged , , , , | Leave a comment

IBE/IBD Contour plots in R

Posted on 18 Jun, 2015 by Arun Sethuraman

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

Posted on 23 Apr, 2015 by Arun Sethuraman

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

Visualizing Linkage Disequilibrium in R

Posted on 9 Apr, 2015 by Arun Sethuraman

Patterns of Linkage Disequilibrium (LD) across a genome has multiple implications for a population’s ancestral demography. For instance, population bottlenecks predictably result in increased LD, LD between SNP’s in loci under natural selection affect each others rates of adaptive evolution, selfing/inbreeding populations … Continue reading →

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

A transcriptomic approach for reduced representation in population genomics

Posted on 6 Apr, 2015 by Melissa DeBiasse

                    Many population genomics studies use methods that provide a reduced representation of the genome, for example RADseq or UCEs. Targeting a subset of the genome reduces the cost of sequencing … Continue reading →

Posted in genomics, howto, methods, Molecular Ecology, the journal, next generation sequencing, RNAseq | Leave a comment

F-statistics Manhattan Plots in R

Posted on 26 Mar, 2015 by Arun Sethuraman

Characterizing differentiation across individual genomes sampled from different populations can be very informative of the demographic processes that resulted in the differentiation in the first place. Manhattan plots have grown to be very popular representations of genome-wide differentiation statistics in … Continue reading →

Posted in bioinformatics, genomics, howto, population genetics, R, software | Tagged , , | 4 Comments