Introduction to PhyloWiki

PhyloWiki was originally developed for use in IB200B: Principles of Phylogenetics, a course offered by the University of California, Berkeley's Department of Integrative Biology. The owner/admin is Nicholas J. Matzke.

PhyloWiki is now a general-purpose phylogenetics/biogeography help wiki, where Nick can upload code updates, tutorials, slides, etc., as well as FAQ pages on R projects like BioGeoBEARS, BEASTmasteR, TNTR, etc. The IB200b pages will be maintained as a resource (but probably not updated further).

R packages

BioGeoBEARS — inference and model choice in historical/phylogenetic biogeography. See also Publications using BioGeoBEARS.

rexpokit — accessory package for BioGeoBEARS, does fast matrix exponentiation with the FORTRAN package EXPOKIT (Sidje 1998)

cladoRcpp — accessory package for BioGeoBEARS, does fast calculation of biogeographic change probabilities for triplets of ancestor, left- descendant, and right-descendant geographic range states at cladogenesis events on a phylogeny. Makes use of Rcpp for this purpose.

TNTR — functions and scripts for converting data and trees from R into TNT format, running TNT analyses, and parsing the results back into R (and then conversion to standard formats and graphics).

BEASTmasteR — Converting NEXUS data files into Beast2 XML for phylogenetic dating analyses using fossils as tips.

modiscloud — a package for processing MODIS Cloud Product data. For the paper on Costa Rican cloud forests, by Goldsmith, Matzke, & Dawson (2013), Ecology Letters.

mod09nrt — Extraction of Bands from MODIS Surface Reflectance Product MOD09 NRT. This package uses some code from modiscloud, so they made me a co-author.

Rloose — Loose scripts that I don't want to lose.

Links to pages in use

Berkeley Biogeography 2020BioGeoBEARS lab for a U.C. Berkeley biogeography course on November 6, 2020

Quantitative Biology — A new course at the University of Auckland in 2020

Introduction to R & PCMs — For BIOINF702 at the University of Auckland

Tree-thinking with R — A lab exercise for the University of Auckland's BioSci 109 course introducing Ecology & Evolution

Explore genome size data — Part of a lab exercise for the University of Auckland's BioSci 210: Evolution course

BioGeoBEARS Workshops — dates, times, and abstracts of BioGeoBEARS workshops, past and future

BEASTmasteR Workshops — dates, times, and abstracts of workshops involving BEASTmasteR (they may include other topics as well), past and future

Matzke 2015 Science Paper On The Evolution Of Antievolution — This paper in Science, published online on December 17, 2015, contains a tip-dated, sampled-ancestors phylogenetic analysis of U.S. creationist/antievolution bills from 2004-2015. (Tracing how creationism involves!) The PhyloWiki page archives bonus material, including a free preprint, figures under Creative Commons license, and supplemental data and code.

TNTwiki — The old help wiki (original / Wayback Machine partial archive) for the (very fast!) cladistic parsimony program TNT has apparently permanently died. This is something of a crisis for people as the TNT command structure is very obscure, and the wiki was almost the only help. I will attempt to re-create the basic of the help at TNTwiki. Feel free to add to it (you may have to email me to get access to PhyloWiki).

2014 Summer Research Experiences (SRE) at NIMBioS for Undergraduates and Teachers

Animations — example animations

PhyloBasics — PhyloBasics is a page for accumulating basic mini-scripts in R for phylogenetics

Abstracts for presentations by Nicholas J. Matzke — annoyingly, in meeting websites, the abstracts are usually (a) hard to find, (b) hard to google, and (c) disappear at some point. This is a huge pain when even the author tries to find them later. So, I will archive mine here.

International Biogeography Society poster on results from biogeographic model testing in my R package BioGeoBEARS.

Phylogenetics help

Sometimes, it is useful to archive phylogenetics tips, tricks, and help. An organizational page for this is phyloHelp. Current example: TNT (Tree analysis using New Technologies), a parsimony program that is famous for being very fast, but for having a very obscure command syntax.

IB200b labs

Methodological Workshop on Biodiversity Dynamics — for: "Evolution of Life on Pacific Islands and Reefs: Past, present, and future", May 26, 2011

mb notes — Notes on usage, quirks, misunderstandings etc. I have noticed with MrBayes 3.2.5 analyses. Mostly for my own memory. YMMV (your mileage may vary) by setup, dataset, MrBayes version, etc.

Dependency hell — When I figure out a successful install of something that gave problems, I'll put it here.


Fun with hominin cranial capacity through time

Frequency of phylogenetics and SDMs in the literature, via SCOPUS (updated)

Matzke 2015 Science paper on The Evolution of Antievolution Policies

Junk DNA debate

Peter Foster's "Idiot's Guide to the Zen of Likelihood"

Main point

Initially the site will be used to post tutorials on how to use R, and how to run various common phylogenetics programs.

However, the wiki may also be used for purposes like:

  • instructions and notes on installing phylogenetics software
  • posting solutions (code) for various tasks in e.g. R, Python, etc.
  • other collaborative projects involving research or education in evolutionary biology

My hope is that the site will become a general resource for the community of researchers and students in phylogenetics and evolution.

Basic rules to help this happen:

  • Users must register with wikidot to add or edit pages, so that we know who is doing what. Registration is open, I will not manually check registrants.
  • I do strongly recommend that users make their username resemble their real name or email. This
      • (a) allows you to get credit for the work you do;
      • (b) allows readers to check the authority of the authors;
      • (c) hopefully, will cut down on the kinds of juvenile activity that tend to arise in anonymous situations, e.g. blog comments
  • This wiki uses a Creative Commons ShareAlike license. This means that contributors are releasing their content for creative re-use, but they also retain copyright to anything they write. Thus, for example, it is appropriate to gradually develop a paper on a topic here, making it available to students and other readers while it is in progress (and perhaps attracting co-authors — main authors should use page permissions, explicit instructions, etc., if they don't want this to happen), and then take their own text and work it up into a final paper for submission to e.g. a journal.
  • Spam, ranting and raving, vandalism, etc., will result in instant banning.

Animation of the geographical history of the Hawaiian Islands / Emperor Seamounts Chain. Produced via an R script, relying on data provided by Clague 1996.


Nick's Projects


Nick's Random Notes

Notes on the wikidot site

File nameFile typeSize
395lab.zipZip archive data54.26 MBInfo
BioGeoBEARS_1.1.3.tar.gzgzip compressed data17.33 MBInfo
foster01-idiotslikelihood.pdfPDF document179.52 kBInfo
Foster_2001_Idiots_guide_to_likelihood.pdfPDF document179.52 kBInfo
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