2020

New updates for PIrANHA, close to new release 2020/12/14

New Gist on reasons to prefer CLI software vs. GUIs 2020/12/13

First Markdown post using Bear app 2020/01/15

How to check Java version and JDK version on Mac 2020/01/05

2019

Problems with locate after Homebrew update on Mac 2019/12/31

2018

Installing gbs2ploidy and its rjags dependency in R on CentOS Linux 2018/08/01

How I moved my blog from Wordpress to a blogdown blog deployed by Netlify 2018/08/01

How I moved my website from Wordpress to GitHub Pages 2018/07/29

Picking a custom search engine for your website 2018/07/25

How to find common variants in multiple VCF files 2018/07/25

First blogdown post 2018/07/16

R install for user on a CentOS Linux supercomputer 2018/03/26

dDocent install successes & failures on Linux supercomputers 2018/03/10

Testing hypotheses of Panamanian frog & fish diversification - now out @ PeerJ Preprints 2018/03/07

stdio.h file error during C/C++ software compilation on Mac 2018/03/06

Command line trash: how to delete, trash, and inspect files from the CLI 2018/03/06

2017

A Very Darwin Christmas: Reminder to Evolutionary Biologists to Never Stop Exploring! 2017/12/26

How To Setup A Linux Supercomputer for RAD-seq 2017/09/17

Analyzing ddRADseq Data in SNAPP 2017/09/13

Running AMOVA (analysis of molecular variance) on biallelic SNP data in R 2017/08/18

Getting BEAST2 Path Sampler analyses running on Windows 10 2017/08/17

Data mining resources for species distribution modeling and macroecology 2017/06/28

2016

Setting DNA substitution models in BEAST 2016/10/11

Automatically install or update all phylogenetics packages in R 2016/04/06

How to kill an R process without forcing R to quit on mac 2016/04/06

Latest *BEAST trace: Most beautiful thing I've seen today 2016/03/11

Getting BEAST v1.8.3 running! Beagle, CUDA, Java, and LINUX 2016/03/10

Dealing with negative phylogenetic branch lengths in BEAST starting trees 2016/03/01

New version of BEAST--v1.8.3--released! 2016/02/22

2015

Update: BEAST v2.3.2 released! 2015/12/17

Update to BEAST v2.3.1 2015/12/02

Cochrane's Aphorism for Molecular Ecologists 2015/11/25

Bagley's Law of Scientific Publication Access 2015/11/23

Detecting trait-dependent shifts in DNA sequence evolution with traitRate 2015/09/17

Coding general data types with ambiguities in BEAST input files 2015/09/08

Stupid common names: Tigerfish 2015/09/02

A funny thing about IMa2 output (a lost 2011 blog post) 2015/09/01

Update: 'new' functions for generating starting trees for BEAST or *BEAST in R 2015/08/30

Get the latest version of BEAST - v2.3.0 - then ask, "Do you need it?" 2015/08/28

Update Mesquite with plugin for reading and writing NeXML format 2015/08/23

Meeting opportunity: Dating species divergences using rocks and clocks 2015/08/07

Update to latest version of BEAST2 - v2.2.1 2015/03/26

2014

New BEAST2 Tutorial that Rocks! 2014/12/27

Alternative ways to quickly get post-burnin trees from BEAST output from the command line 2014/12/26

Give your mac some relief: how to remove the sleepimage file using Terminal 2014/09/20

Updated links to BEAST 1.7.5 phylogeography tutorials 2014/08/07

Mesquite website down yesterday, today... and tomorrow? 2014/08/07

New book on phylogenetic comparative analysis in R 2014/04/30

Cool new paper on phylogenetic community diversity in Costa Rican ants 2014/04/30

New web server update for Bayesian PTP species delimitation on single-locus gene trees - and more! 2014/03/07

So you got a starting tree? How to add it to your BEAST2 xml file and make it work for you 2014/02/17

Lower Central America phylogeography: review paper gets 100 views in 2 days on Academia.edu! 2014/02/08

2013

New version of Lamarc--Lamarc v2.1.9--now available! 2013/12/13

New version of Tracer - Tracer v1.6 - now available! 2013/12/11

Luke Mahler visits BYU 2013/12/11

New Phyloseminar with Daniel Ksepka: adding fossil data to phylogenies 2013/12/03

Where to outsource next-generation sequencing runs for de novo SNP discovery for phylogenetics and phylogeography 2013/11/27

Bryan Carstens's phylogeography talk from the 2012 Molecular Ecology Symposium, 1st Joint Congress on Evolutionary Biology, Ottawa, Canada 2013/11/27

Software Carpentry: providing training and open-access material for self-paced instruction in software skills for researchers 2013/11/18

Tracy Heath visits BYU Biology dept ... and more 2013/11/12

California freshwater fish distribution resources 2013/11/11

BEASTGen: a new program for creating NEXUS, FASTA and BEAST XML input files for phylogenetics software 2013/10/29

Symphony of Science - The Greatest Show on Earth! A music video about E... 2013/10/27

A comprehensive list of phylogenetics packages for R 2013/10/27

Do journal guidelines discouraging single-locus papers reflect an attitude that contributes to a "file-drawer problem" in phylogeography and phylogenetics? 2013/10/25

Off to a good start: how to generate starting trees for BEAST analyses using R 2013/10/10

SSH clients and Linux command line for interacting with supercomputers during evolutionary analysis 2013/03/13

2011

R functions for working with phylogenetic trees in packages ape, geiger, and caper: Part I 2011/11/22

Statistical phylogeography tutorial #1: Coalescent simulations in Mesquite Part I 2011/09/22

Migrate-N and phylogeography: Bayesian priors and run settings 2011/09/13

DNA polymorphism indices and sampling 2011/09/04

BEAST and the BEAST basics: molecular clocks and how to input rates into BEAST 2011/09/01

Estimated cytb and RPS7 mutation rates for Heterandria 2011/08/12

jmodeltest will not run with single quotes around tip names 2011/08/06

New GARLI web server for runs in the cloud 2011/08/05

Evolution, phylogenetics, and phylogenetic model selection: jmodeltest vs. DT_ModSel 2011/08/05

In only so many words... 2011/07/19

One way to evaluate incomplete lineage sorting in your phylogenetic or phylogeographic data 2011/07/19

2010

How to use MIGRATE-N for phylogeography 2010/09/04

Phylogenetic hypothesis testing 2010/08/16

Phylogenetic signal 2010/08/07

Recent stuff - latest Micropterus sequences on GenBank 2010/08/03