Collaborations

Special Links

Presentations

Notice: The slides listed below are mostly in Chinese.
  • Introduction to Phylogenetic Comparative Methods: One day workshop at Beijing Forestry University  (Slides) (BJFU) 2012, New
  • Evolutionary Ecology and R: An introduction to phylogenetic comparative methods (PDF) (Renmin University, Beijing) 2011
  • Ice Break of R: An Introduction to R statistical Programming Language (PDF) (KFBG, Hong Kong)  2011
  • An introduction of R: statistical programming and plotting (PDF) (IBCAS, Beijing) 2010
  • Analyzing the evolution of niches: Principles and Methods (PDF) (Xiamen Uinversity, Fujian, China) 2010
  • Phylogenetic tree inferences: from DNA sequences to divergence time (PDF) (IBCAS, Beijing) 2010
  • Tutorials of Phylomatic and Phylocom (together with traits dendrograms) (PDF) (IBCAS, Beijing) 2010

Tutorials (in Chinese)

Top Journals

Online Courses 

The Anthro Tree Website
http://nunn.rc.fas.harvard.edu/groups/pica/

___Bayesian Inferences Lectures by P. Lam
http://www.people.fas.harvard.edu/~plam/teaching.html

Review Course: Markov Chains and Monte Carlo Methods
http://users.aims.ac.za/~ioana/

Bayesian Methods
http://voteview.com/Bayes_ucsd.htm

Machine Learning
http://disi.unitn.it/~passerini/teaching/2010-2011/MachineLearning/

Bayesian Networks and Graphical Models
http://www.dina.dk/phd/s/s6/

Doing Bayesian Data Analysis
http://www.indiana.edu/~kruschke/RobustBayesianComparison/
http://www.indiana.edu/~kruschke/
http://www.indiana.edu/~jkkteach/

Stat 295 Bayesian Inferences
http://bayesrules.net/stat295.html

Bayesian Analysis for the Social Sciences
http://jackman.stanford.edu/classes/BASS/

Statistical Phylogeography
http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography

PCM at Universite de Lausanne
http://www2.unil.ch/phylo/teaching/pmc.html

Integrative Biology at UC Berkeley
Principles of Phylogenetics: Ecology and Evolution
http://ib.berkeley.edu/courses/ib200b/

Principles of Phylogenetics: Systematics
http://ib.berkeley.edu/courses/ib200a/

EEB courses on Ecology
http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB_2244/2244W_Ecology_Spring_2010

Phylogenetics (EEB)
http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Phylogenetics:_Syllabus

Principles and Methods in Systematic Biology
http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Principles_and_Methods_of_Systematic_Biology_%28EEB_5347%29

Quantitative methods in Ecology and Evolution by Prof. Schluter (UBC)
http://www.zoology.ubc.ca/~schluter/bio548/

Principles and Practice of Phylogenetic Systematics
http://www.faculty.biol.ttu.edu/Strauss/Phylogenetics/LectureNotes.htm

R workshop for phylogenetic comparative methods
http://www.webpages.uidaho.edu/~lukeh/rFiles.html

Phylogenetic Comparative Methods
http://systematics.mortonarb.org/lab/teaching/pcm35300.readings.html

Biodiversity analysis by Dr. He Fangliang
http://www.ualberta.ca/~fhe/people.html

Statistical Methods in Ecology
http://www.unc.edu/courses/2010fall/ecol/563/001/index.html

Statistics for Ecology and Evolution 2008 By Dr. Jack Weiss
http://www.unc.edu/courses/2008fall/ecol/563/001/index.html

Likelihood Methods in Ecology by Prof. Charles Canham
http://www.ecostudies.org/lme.html

Systems Ecology, Methods of Ecological Modeling By McCarthy et al.
http://classes.warnercnr.colostate.edu/nr575/lecture-schedule/

An Introduction to R: Software for statistical modelling and Computing, Course Notes
http://www.csiro.au/resources/Rcoursenotes.html

Introduction to Statistical Computing by Ross Ihaka
http://www.stat.auckland.ac.nz/~stat782/?Statistics_782

Biostatistics-Statistical Computing by Gonçalo
http://www.sph.umich.edu/csg/abecasis/class/

Basic Population Genetics (and a plenty of resources)
http://www.dorak.info/genetics/popgen.html

Biology Textbook
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/W/Welcome.html

Genomic Variation Lab
http://genome-lab.ucdavis.edu/Links/ECL%20290%20Winter%202007/index.htm

Linkage Disequilibrium Analysis
http://www.nslij-genetics.org/ld/index.html

The Online Biology Book
http://ridge.icu.ac.jp/biobk/biobooktoc.html

Coalescent Theory and Applications
http://web.eve.ucdavis.edu/pbg298/

R resources

R project
http://cran.r-project.org/

R-Graphical Manual
http://bm2.genes.nig.ac.jp/RGM2/index.php

R resources at NCEAS
http://www.nceas.ucsb.edu/scicomp/software/r
http://www.nceas.ucsb.edu/scicomp/documents

R-phylo Wiki
http://www.r-phylo.org/wiki/Main_Page

R Hackathon
https://www.nescent.org/wg_phyloinformatics/R_Hackathon_1

Analysis of Community data using R
http://ecology.msu.montana.edu/labdsv/R/labs/

F. Farrell’s R resources
http://biostat.mc.vanderbilt.edu/wiki/Main/RS

R Tutorial by Dong-Yun Kim
http://www.math.ilstu.edu/dhkim/Rstuff/Rtutor.html

R Programming for APTS Students at Oxford University by Prof. R. Ripley
http://www.stats.ox.ac.uk/~ruth/

Statistics with R
http://zoonek2.free.fr/UNIX/48_R/all.html

Crantastic
http://crantastic.org/

R-Tips
http://pj.freefaculty.org/R/Rtips.html

Packfor at R forge
http://r-forge.r-project.org/R/?group_id=195

Geographical Data Analysis using R
http://geography.uoregon.edu/geogr/index.html

Create Maps with R geographical Classes 
http://www.nceas.ucsb.edu/scicomp/usecases/CreateMapsWithRGraphics

Applied Spatial Statistics in R
http://www.people.fas.harvard.edu/~zhukov/spatial.html

Software for Phylogenetic Comparative Methods

BodegaWiki
http://bodegaphylo.wikispot.org/Topics

Joe Felsenstein’s comprehensive list for Phylogenetic software
http://evolution.genetics.washington.edu/phylip/software.html

Software by Agapow
http://www.agapow.net/software

PAUP*
http://paup.csit.fsu.edu/

CLUSTAL
http://www.clustal.org/

MUSCLE
http://www.ebi.ac.uk/Tools/msa/muscle/

MrBayes
http://mrbayes.csit.fsu.edu/

RAxML
http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm

BEAST, FigTree, PhyloGen and Tracer
http://tree.bio.ed.ac.uk/software/

MEGA
http://www.megasoftware.net/

r8s
http://loco.biosci.arizona.edu/r8s/

multidivtime
http://statgen.ncsu.edu/thorne/multidivtime.html

Mesquite
http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/manual.html

Phylocom
http://www.phylodiversity.net/phylocom/

APE
http://ape.mpl.ird.fr/

Lagrange
http://www.bioinformatics.org/~rick/software.html
http://www.reelab.net/home/node/38
http://code.google.com/p/lagrange/

laser
 http://cran.r-project.org/web/packages/laser/index.html

Phylis
http://www.eve.ucdavis.edu/rcthomson/phylis/

Biolinux
http://nebc.nox.ac.uk/tools/bio-linux/bio-linux-5.0

Software for Population Genetics

__ Statistical Phylogeography
http://darwin.eeb.uconn.edu/wiki/index.php/Statistical_phylogeography

CREATE
https://bcrc.bio.umass.edu/pedigreesoftware/node/2

PGDSpider
http://www.cmpg.unibe.ch/software/PGDSpider/

popabc: infer historical demographic parameters
http://code.google.com/p/popabc/

DIYABC
Approximate Bayesian Computation for inference on population history using molecular markers
http://www1.montpellier.inra.fr/CBGP/diyabc/

Software by Jody Hey
http://genfaculty.rutgers.edu/hey/software

LAMARC – Likelihood Analysis with Metropolis Algorithm using Random Coalescence
http://evolution.genetics.washington.edu/lamarc/index.html

MIGRATE-N estimation of population sizes and gene flow using the coalescent
http://popgen.sc.fsu.edu/Migrate/Migrate-n.html

PhyloMapper
http://www.evotutor.org/PhyloMapper/

SSA Inference of Maximum Likelihood phylogenetic trees using a stochastic search algorithm
http://www.stat.osu.edu/~lkubatko/software.html

BEST Bayesian Estimation of Species Trees
http://www.stat.osu.edu/~dkp/BEST/introduction/

BEAST Tracer, BEAGLE
http://beast.bio.ed.ac.uk/Main_Page

GEODIS: A tool to perform the nested clade phylogeographic analysis (NCPA)
http://darwin.uvigo.es/software/geodis.html

Diffusion Approximation for Demographic Inference
http://code.google.com/p/dadi/

Genetic Landscapes GIS Toolbox: Tools to create genetic divergence and diversity landscapes in ArcGIS
http://www.werc.usgs.gov/productdetails.aspx?id=4017

TESS 2.3: Bayesian Clustering using tessellations and Markov models for spatial population genetics
http://membres-timc.imag.fr/Olivier.Francois/tess.html

Geneland: process individual multilocus genetic data to detect population structure
http://www2.imm.dtu.dk/~gigu/Geneland/

ABC4F Approximate Bayesian Computation for F-statistics
BIMr  (Bayesian Inference of imMigration rates. A new Bayesian method to identify the environmental factors that influence recent migration).
COLONISE  a user-friendly Microsoft? Windows software for the study of colonisation events in natural populations.
GENBMAP
GESTE (GEnetic STructure inference based on genetic and Environmental data) is a Bayesian method
PARENTE  computer program for parentage analysis
ScanAFLP a R script to evaluate AFLP electropherograms for phenotyping and marker selection
WOMBSOFT Wombling-based that analyse individually geo-referenced multilocus genotypes for the inferences of genetic boundaries between populations.
http://www-leca.ujf-grenoble.fr/logiciels.htm

Software by Rannala research Group
http://www.rannala.org/?page_id=13

Structurama
http://cteg.berkeley.edu/~structurama/

Structure
http://pritch.bsd.uchicago.edu/structure.html

Software by Dr, Mark Beaumont
http://www.rubic.rdg.ac.uk/~mab/home.html

Software by Dr. Michael G. B. Blum
http://membres-timc.imag.fr/Michael.Blum/index.html

popABC
http://code.google.com/p/popabc/

Rejector
http://www.stanford.edu/~mjobin/rejector/Rejector/Home.html

msBayes
http://msbayes.sourceforge.net/

EggLib
http://egglib.sourceforge.net/installation.html
 

Software for Ecological Modelling , Biogeography & Conservation

Forward Selectoin
http://r-forge.r-project.org/R/?group_id=195

SAM
http://www.ecoevol.ufg.br/sam

DIVA-GIS
http://www.diva-gis.org/

Biodiverse
http://code.google.com/p/biodiverse/

C-Plan
http://www.uq.edu.au/~uqmwatts/cplan.html/

LQGraph
http://uts.cc.utexas.edu/~consbio/Cons/

MARXAN
http://www.ecology.uq.edu.au/index.html?page=27710

MultCSync
http://uts.cc.utexas.edu/~consbio/Cons/

NatureServe Vista
http://www.natureserve.org/prodServices/vista/overview.jsp

Surrogacy
http://uts.cc.utexas.edu/~consbio/Cons/

ZONATION
http://www.helsinki.fi/bioscience/consplan/

WORLDMAP
http://www.nhm.ac.uk/research-curation/research/projects/worldmap/

EcoSim
http://www.garyentsminger.com/ecosim/index.htm

EstimateS
http://viceroy.eeb.uconn.edu/EstimateS

Mid-domain Null
http://www.nceas.ucsb.edu/~mccain/

GDM
http://www.biomaps.net.au/gdm/

PAST
http://folk.uio.no/ohammer/past/

RangeModel
http://viceroy.eeb.uconn.edu/RangeModel

BIOMAPPER
http://www2.unil.ch/biomapper/

DesktopGarp
http://www.nhm.ku.edu/desktopgarp/

Lifemapper
http://www.lifemapper.org/

GRASP
http://www.cscf.ch/grasp/

MAXENT
http://www.cs.princeton.edu/~schapire/maxent/

GIS Software and Data
http://macroecology.ku.dk/resources/gis-software/

Evolutionary Biology & Ecology Universitel Libre de Bruxelles
http://ebe.ulb.ac.be/ebe/ebe-Welcome.html
Last update: 14-Oct-2014
© Jinlong Zhang. All rights reserved.