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    ART    
  My favourite Van Gogh
• The WebMuseum: definitely the best resource out there for online art. Though it may not have every artist and every painting you can think of, it is the best collection I have seen yet.
• The Artchive: for those artists and paintings missing above, check here.
• The Museum of Modern Art (MoMA).
• The Guggenheim Museums.
My favourite painter, Turner  
RESEARCH RESOURCES
Software Links
Arlequin3 (Laurent Excoffier, Guillaume Laval, and Stefan Schneider): an exploratory population genetics software environment with a Java graphical interface that can be implemented either at the intra-population or at the inter-population level. Windows only.
BayesAss (Greg Wilson and Bruce Rannala): Bayesian estimation of recent migration rates. Similar to Structure, except doesn't assume Hardy-Weinberg, and so is useful in assigning recent (2-3 generations) migrants. Multiple platforms.
BEAST (Alexei Drummond and Andrew Rambaut): Simultaneous Bayesian estimation of phylogeny and divergence time. Does not require the assumption of autocorrelated rates of substitution across a tree, and allows for arbitrarily complex partitioning strategies. Multiple platforms.
BioEdit (Tom Hall): a biological sequence alignment editor involving several sequence manipulation and analysis options and fully-automated links to local and WWW-based anaylsis programs. The best alignment editor I have seen. Unfortunately only available for Windows machines, and development has been discontinued.
Bio-Perl (various): an extremely powerful Perl 5 module used for bioinformatics. Available on any platform Perl can be installed.
Bio-Phylo (Rutger Vos): Similar to Bio-Perl in structure and ease-of-use, but geared towards analyzing and manipulating phylogenetic trees. Available on any platform Perl can be installed.
Bottleneck (Sylvain Piry, Jean-Marie Cornuet, and Gordon Luikart): a coalescent-based method for the detection of genetic bottleneck signatures. Tests for a transient elevated level of heterozygosity relative to what is expected under mutation-drift equilibrium. Requires only a single sample from a population. Informative for 2-4Ne generations. Available in french or english for PC.
BottleSim (Chih-Horng Kuo): a very user-friendly application for the simulation of realistic bottleneck scenarios. In addition to specifying the magnitude and duration of bottleneck, allows input of many important parameters (life span, age of reproduction, generation overlap, mating system, sex ratio). Mac or PC.
Convert (Jeff Glaubitz): the best format conversion program out there for diploid data. Outputs files for GDA, Genepop, Arlequin, Popgene, Microsat, Phylip, and Structure. PC only.
GARLI (Derrick Zwickl):a genetic algorithm approach to maximum likelihood inference of phylogeny. Superior to rival MetaPIGA in terms of likelihood calculation and complexity of the models supported (GTR+I+G by default). The current incarnation supports only a single population of trees. Very fast. Can run in parallel.
GeneClass (J.-M. Cornuet, D. Paetkau, L. Baudouin, A. Estoup, S. Piry, and A. Alapetite): in my eyes, the best assignment package out there for analyses with pre-defined populations (although this 'pre-definition' should reflect data, and not the assumptions of the investigator). Offers several different assignment methods (genetic distance, allele frequencies, Bayesian criteria), nice interface, and speedy analyses. PC or Linux platforms.
HP-RARE (Stephen Kalinowski): uses rarefaction to accomodate differences in sample sizes when estimating indices of diversity and private alleles. Allows hierarchical sampling. PC only.
HyPhy (S. L. Kosakovsky Pond and S. V. Muse): an enormously powerful ML package that allows the testing of myriad evolutionary hypotheses, and to this end includes tools for data simulation. Supports partitioned models of evolution. Multiple platforms supported.
LAMARC (various): a coalescent-based package of programs for computing population parameters, such as population size, population growth rate and migration rates by using likelihoods for samples of genetic data from populations. Includes the programs Migrate, Fluctuate, Recombine, Lamarc and Coalesce.
MacClade (David Maddison and Wayne Maddison): a computer program that provides tools for the graphic and interactive analysis of molecular and morphological data, phylogeny, and character evolution. MacClade reconstructs and displays character evolution on the phylogenetic tree and gives feedback via tree graphics, statistics, and charts. Also very useful in constructing PAUP blocks for use in PAUP*.
MEGA4 (Sudhir Kumar, Koichiro Tamura, and Masatoshi Nei): a program for phylogenetic reconstruction and tests of molecular evolution. Though lacking the likelihood analyses of PAUP*, it works quite well for distance, minimum evolution and parsimony analyses. Multiple platforms supported.
Mesquite (Wayne Maddison and David Maddison): across-platform modular system for evolutionary analysis. I have not found the time to explore this fully, but it looks very promising.
Modeltest (David Posada): used in conjunction with with PAUP*, Modeltest helps a user to choose the model of DNA substitution that best fits his/her data, among 56 possible models. This is accomplished through an implementation of hierarchical likelihood ratio tests and the AIC criterion.
MrBayes3 (Fredrik Ronquist and John Huelsenbeck): the program for Bayesian inference of phylogeny. This represents the standard of phylogenetic analysis, particulary because of speed (via MCMCMC) and ease of interpretation. Multiple platforms supported.
Multidivtime (Jeff Thorne): a Bayesian modelling of among-lineage rate variation for the purpose of phylogenetic dating. Assumes an autocorrelation of substitution rates from ancestor to descendent branches (although this autocorrelation can break down with long branch lengths. Supports multiple genes and multiple temporal constraints. Unix.
PAML (Ziheng Yang): a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Of importance is it allows the ML analysis of amino acid sequences, which PAUP* does not currently do.
PAUP* (David Swofford): if you are not familiar with PAUP*, you are not a molecular phylogeneticist.
PHYCAS (Paul Lewis, Mark Holder, and David Swofford): a soon-to-be released open-source phylogenetic analysis package.
PHYLIP (Joseph Felsenstein): a free package of programs for inferring phylogenies. Again, if you are not familiar with PHYLIP, you are not a molecular phylogeneticist.
Phylogeny Programs: an amazing list of phylogeny packages cross-referenced by method, computer system, data type, etc. Compiled and maintained by Joseph Felsenstein.
r8s (Michael Sanderson): a penalized likelihood rate-smoothing approach to phylogenetic dating in the face of rate heterogeneity. Single gene only, but multiple temporal calibrations. Offers sequence or fossil-based cross validation. Allows analysis of bootstrapped trees for the estimation of 95% confidence intervals on inferred dates. Unix.
RAxML (Alexandros Stamatakis): a very fast maximum likelihood phylogeny reconstruction program, written explicitly for the analysis of large (several thousand taxon) data sets. Very nice options are partitioned substitution models, parallel implemention, and the use of constraint trees.
Structure (Jonathan Pritchard): a Bayesian assignment software package. Identifies distinct populations and probable migrant history of all individuals. Most importantly, Structure does not require a priori definition of populations (in my eyes, the biggest problem in population genetics today).
 
Labs
Resources
 
EvolDir: the Evolution Directory - a list server for evolutionary biologists. Used for circulation of software developments, jobs, conferences, general queries, etc.
Avian mtDNA primers: compiled by Michael Sorenson.
Workshop on Molecular Evolution: held at Woods Hole, this was the highlight of my academic career to date. Highly recommended.
Summer Institute in Statistical Genetics: held at NC State. Also highly recommended.
TreeBASE: a database of published phylogenetic trees and data matrices.
NESCent: the National Evolutionary Synthesis Center.
AVECOL: a listing of museum bird collections, links to searchable collections.
NCBI: the phenomenal genetic sequence database.

CIPRES: access to the cluster housed at the San Diego Supercomputing Center.
 
UNIVERSITY OF MICHIGAN, Ann Arbor, Michigan
• My Biology 162 Lab webpage (Michigan): schedule, readings, and notes.
Department of Ecology and Evolutionary Biology (EEB)
• University of Michigan Museum of Zoology (UMMZ)
WCBN: the coolest radio station out there, broadcasted from the University of Michigan.
MIRLYN: the University of Michigan library catalogue.
CAC: the Center for Advanced Computing.
UofM
 
QUEEN'S UNIVERSITY, Kingston, Ontario
Queen's University Conservation Genetics Group: a summary of the group membership, current projects, facilities, etc.
Department of Biology: a link to Department of Biology at Queen's University.
HPCVL: The High Performance Computing Virtual Laboratory (HPCVL) was formed by a consortium of four universities located in Eastern Ontario, including Queen's. Important to our lab principally for running massive analyses of genetic data using the program Migrate.
Behaviour, Ecology, and Evolution Research Seminars (BEERS): seminars put on by graduate students and postdocs in a comfortable alcohol saturated atmosphere.
• My Biology 206 Lab webpage (Queen's): schedule, readings, and notes. Old.
  Queen's  
GUITAR RESOURCES
Picasso    
 

Sonic Youth: Most releases available, including tuning guide.
Lou Reed/Velvet Underground: A searchable archive of his entire career.
Guided By Voices/Robert Pollard: Organized by band and album.
David Bowie: Covers many of his studio albums.
Bob Dylan: Mostly chords, but fairly complete.
Jethro Tull: Album-by-album break down - very good.
Pink Floyd: Includes studio albums, solo albums, rarities, lessons and more.
Classical Guitar Tablature: The best on the web.
Frank Black/Pixies: Organized by band and album.
Ani DiFranco: Nearly 100 tabs from 13 albums.
Guitarnotes: Tabs, lessons, shopping, etc. - eveything that has anything to do with guitars.

   
ENTERTAINMENT
• The offical Sonic Youth website.
• The offical Frank Zappa website.
• The offical Iggy Pop website: he grew up in Ypsilanti!
• The offical Guided By Voices website.
• The offical Robert Pollard website.
• The offical Yo La Tengo website.
• The offical Ween website.
• The offical David Bowie website.
  Binoculars
• Bruce Bowman's Southeast Michigan birding resource. Checklists, maps, photos, statistics, etc. Amazing resource.
xkcd: a "webcomic of romance, sarcasm, math, and language."
PhD (Piled Higher and Deeper): a comic strip recounting the trials and tribulations of being a graduate student.
Nova: my favourite program on PBS.
Joseph Wu's origami page - the best out there by far.
Origami Database - the best available.
• A blog of My Family (Rachel, Calliope, and Nova Brown).
MarathonGuide.com - a listing of races all over the world.
Can't Get Enough Futurama: My favourite show, ranking up there with Rocky and Bullwinkle.
• The official Douglas Adams website: everything you've ever wanted to know about this remarkable writer.
• Alta Vista's Babel Fish translation service. Translate text or webpages between 8 languages.
 
JD Salinger   Homer Sane   Ian Anderson   Zoidberg   Calliope   Peabody and Sherman   Syd Barrett
 
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