Tag Archives: software

What is DAS? A new tool to recover genomes from metagenomes

Posted on 8 Jun, 2018 by Kelle Freel

There are a lot of data out there, and if you haven’t already noticed the ‘omics train has steadily stayed its path through the fruitful (but challenging) world of metagenomics. Metagenomics offers the chance to unravel complex microbial communities without … Continue reading →

Posted in bioinformatics, community ecology, genomics, metagenomics, methods, microbiology, next generation sequencing | Tagged , , , | Leave a 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 →

Posted in bioinformatics, next generation sequencing, software | Tagged , , | Leave a comment

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 →

Posted in software, speciation | Tagged , , , , , | Leave a comment

Data, data everywhere and another tool to use: Taxonomer, a web-tool for metagenomics data analysis

Posted on 26 May, 2016 by Kelle Freel

Because sequencing. With all the affordable genome and metagenome sequencing available, we’ve reached an unprecedented point at which we can profile microbial communities more accurately than ever before. For this reason, it’s essential to develop efficient methods for data analysis. … Continue reading →

Posted in bioinformatics, community ecology, genomics, metagenomics, methods, microbiology, software | Tagged , , , | 1 Comment

Battle of the Text Editors

Posted on 16 Mar, 2016 by Katie Everson

Whether you’re a coding master or a total technophobe, a good text editor is a must-have for the molecular ecology toolkit. Text editors are great for managing code, formatting input files, or jotting notes. But with so many different text … Continue reading →

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

Picking the ripest model with PHRAPL

Posted on 9 Sep, 2015 by Rob Denton

To study patterns of genetic variation is to consider scale. The choices an investigator makes when designing a study can produce such a beautiful breadth of evolutionary patterns: from populations to species, from local to continental, from ancient to contemporary. The fields that … Continue reading →

Posted in methods, phylogeography | Tagged , , | Leave a comment

Isolation by environment explains why the grass isn't always greener

Posted on 3 Dec, 2014 by Rob Denton

Ever since Sewall Wright introduced isolation by distance in 1943, the interplay between genetic differentiation and geographic distance has been a foundational, sometimes frustrating, aspect of population genetics studies. But distance isn’t just distance. The walk to my car isn’t any longer when … Continue reading →

Posted in methods, Molecular Ecology, the journal, population genetics | Tagged , , , | 2 Comments