Category Archives: software

Evolution 2023: Highlights of evolution and ecological genetics at Albuquerque

Posted on 30 Jun, 2023 by Jeremy Yoder

Evolution is back, folks. That is, the 2023 joint annual meeting of the American Society of Naturalists, Society of Systematic Biologists, and Society for the Study of Evolution, held last week in Albuquerque, New Mexico, felt just about like its pre-pandemic self. The … Continue reading →

Posted in community, conferences, ecology, evolution, genomics, software | Tagged , , , | Leave a comment

Metabarcoding for every body, every habitat, every time

Posted on 19 Jul, 2018 by Laetitia Wilkins

The immediate reason why I wanted to write about Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles is its usefulness for the scientific community and the effort of the authors to make their study reproducible. … Continue reading →

Posted in bioinformatics, community, community ecology, DNA barcoding, fieldwork, metagenomics, next generation sequencing, phylogenetics, R | Tagged , , , , , , | 1 Comment

Population genetic simulation … in Lego

Posted on 10 Jul, 2018 by Jeremy Yoder

Julien Yann Dutheil, of the Institut des Sciences de l’Évolution de Montpellier, has a long track record of work in population genetics and genomics methods, particularly in the C++ programming language. He recently posted a video to YouTube, though, which … Continue reading →

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Visualize your genome assemblies

Posted on 18 Dec, 2017 by Elin Videvall

Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily), is a program that creates visualisations of sequence assemblies that you can interact with. When assembling a genome with your favorite assembler, you are usually building graphs, from which … Continue reading →

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NPR's muddled take on scientific racism and direct-to-consumer genetics

Posted on 7 Jul, 2017 by Jeremy Yoder

NPR’s science blog Cosmos & Culture has a post up about a new book on scientific racism and population genetics, particularly in connection with personal genetic ancestry reconstruction like that offered by 23andMe and other “direct-to-consumer” (DTC) genetic testing outfits. … Continue reading →

Posted in politics, STRUCTURE | Tagged , , | 1 Comment

Easily aggregate bioinformatic sample output with one tool

Posted on 3 Jul, 2017 by Elin Videvall

Today I’m going to write about one of my favorite bioinformatic tools, MultiQC. If you’ve used it, you know why, and if you haven’t, prepare to be amazed. Many bioinformatic software produce output on a per-sample basis. That is, you … Continue reading →

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An Update on the Great BAMM Controversy

Posted on 1 Mar, 2017 by Ethan Linck

Update, 01 August 2016, 2:50PM. This post has been updated to include information contained in the supplemental material of Rabosky et al. 2017, and clarify the difference between branch-specific and tree-wide rate variation. Back in August, I summarized the main … Continue reading →

Posted in blogging, evolution, methods, phylogenetics, science publishing, software, speciation | Tagged , , , | Leave a comment

Phylogenetic trees in R using ggtree

Posted on 8 Feb, 2017 by Elin Videvall

Recently, one R package which I like to use for visualizing phylogenetic trees got published. It’s called ggtree, and as you might guess from the name it is based on the popular ggplot2 package. With ggtree, plotting trees in R has … Continue reading →

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

False detection of "true" species under the multi-species coalescent model

Posted on 7 Feb, 2017 by Katie Everson

The multi-species coalescent model (MSCM) is the biggest name in the game (if the game is genetic species delimitation). But a new paper from Proceedings of the National Academy of Sciences asks: is the MSCM really doing what we think it’s doing? Some … Continue reading →

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Unbalanced population sampling and STRUCTURE

Posted on 5 Jan, 2017 by Arun Sethuraman

The utility and intuition offered by the program STRUCTURE, and more generally, the ‘admixture’ model of Pritchard et al. (2000) are unquestioned – with tens of thousands of citations, it retains its lead among the most popular population genetics software. … Continue reading →

Posted in bioinformatics, genomics, howto, methods, population genetics, software, STRUCTURE | Tagged , , | 1 Comment