Websites
The ¨Tree of Life¨
Deep Metazoan Phylogeny
Tree of Life
1K Insect Transcriptome Evolution
Next generation sequencing and analysis
Broad Institute Next Generation Sequencing Workshop Material
Harvard Informatics Training
EBI: Next Generation Sequencing Practical Course
Phylogenetic analyses (alignment, models, reconstruction)
Multiple sequence alignment
Beyond mere multiple sequence alignment by Steven M. Thompson
Data partition
Partition by codon position with Mesquite
PartitionFinder
Model selection/test
[email protected]
JModel@Universidad Del Valle
Mode selection@Bodega Phylogenetics Wiki
Step-to-step guide to Modeltest@NZ Rhizobia
ModelGenerator
FindModel
Model fitting in phylogenetics
Bayesian phylogenetics
An Introduction to Bayesian Phylogenetics by Mike Lee
Maximum likelihood
Maximum Likelihood in Phylogenetics by Paul Lewis
Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data by Paul Lewis
Phylogenetics, applications
Historical Biogeography
Caribbean Research Resources [Permit and travel info]
Island Biogeography [Arachnids of West Indies and Madagascar]
Software, programs, tools
Archaeopteryx [Visualization, Analysis, and Editing of Phylogenetic Trees]
BIO::Phylo
DendroPy Phylogenetic Computing Library
EvolView [easy-to-use tool for displaying, managing and customizing phylogenetic trees]
ExPASy - Bioinformatics Resources Portal
E.T.E [a Python Environment for phylogenetic Tree Exploration]
GenGIS [Link phylogenies and specimen/sequence data with digital maps]
iTOL-Interactive Tree Of Life [phylogeny and data visualization tool]
Jalview [interactive editing, analysis and visualization of multiple sequence alignments]
List of software/programs compiled by Joe Felsenstein
Pablo Vinuesa's collection of evolutionary genomics resour
PLUTo: Phyloinformatic Literature Unlocking Tools
Phylemon2 - Phylogenetic analyses online environment
Phylostatic!
phyloT - generate a phylogeny from NCBI taxonomy
PieTree - display ancestral states on a phylogeny with pie-
Shapesr-phylo.org [phylogenetic comparative methods wiki]
Sequence manipulation suite
SVAMP - Sequence Variation Analysis,Maps and Phylogeny
Treedyn [tree annotation and graphics]
Treegraph [graphical editor for phylogenetic trees]
T-REX [a web server for inferring, validating and visualizing phylogenetic trees and networks]
Phylab [Java applet for teaching phylogenetics] VoSeq [database for storing voucher and DNA sequences]
PhyloWidget [viewing, editing, and publishing phylogenetic trees online]PhyloXML [an XML language designed to describe phylogenetic trees]
Learning materials (courses, workshops)
2nd National Postgraduate Training Workshop in Systematics
ANU PhyloWorkshop [6 Lectures]
Bioinformatics Workshop and Training - List by Stephen Turner
Brown University BIO 1425 "Phylogenetic Biology" by Casey Dunn
DNA sequence based studies of microbial diversity (by Jonathan Eisen)
Current Topics in Phylogenetics [with tutorials on programs]
Essential Cladistics
Evolution and Genomics
Harvard "OEB 181: Systematics" (by Gonzalo Giribet & Charles Marshall)
Iowa State U. "Molecular Phylogenetics"
Kansas University "Phylogenetic Methods"
Kerstin Hoef-Emden - Introduction to Molecular Phylogeny [PDF]
NESCENT Academy
Phylogenetic Reconstruction [Evolution textbook chapter]
Phylogeography: Spatial Evolutionary Genetics (by A. Crawford)
Courses
BYU "Introduction to Phylogenetic Comparative Methods" (by Juan Santos)
Phylometh.org - online phylogenetics course by Brian O'meara
Principles of biological systematics and nomenclature
TAMU "Quantitative Phylogenetics" (by Mariana Mateos & Jim Woolley)
Texas Tech "Principles and Practice of Phylogenetic Systematics"
U. Alaska "Introduction to Biosystematics" (by Derek Sites)
U. Alaska "Systematics and Comparative Biology" (by Derek Sites)
U. Conn. Seminar in Comparative Biology
U. Conn. Phylogenetics (by Paul Lewis)
U. Idaho Principles of Systematic Biology (by Jack Sullivan)
U. Utah "Building Evolutionary Trees: Method, Theory & Controversy"
U. Washington "Phylogenetic Inference" (by Joe Felsenstein)
U. Wisconsin "Phylogenetic Analysis of Molecular Data" (David A. Baum)
Various Guides to Molecular Phylogenetics by Peter Unmack
Research labs and groups
Phylogenetics
Stockholm Phylogenomics Group
Zoological Systematics and Evolution, Barcelona, Spain Phylodiversity.net
Phylogenetics - applied research
SPSAS-evo
Beetles
Water and Cave Beetle Evolution Lab (Spain, CSIC)
Andrew Short's lab (aquatic beetles), Kansas University
Social media
Phylobabble [discussion forum for phylogenetic theory and applications]
Deep Metazoan Phylogeny
Tree of Life
1K Insect Transcriptome Evolution
Next generation sequencing and analysis
Broad Institute Next Generation Sequencing Workshop Material
Harvard Informatics Training
EBI: Next Generation Sequencing Practical Course
Phylogenetic analyses (alignment, models, reconstruction)
Multiple sequence alignment
Beyond mere multiple sequence alignment by Steven M. Thompson
Data partition
Partition by codon position with Mesquite
PartitionFinder
Model selection/test
[email protected]
JModel@Universidad Del Valle
Mode selection@Bodega Phylogenetics Wiki
Step-to-step guide to Modeltest@NZ Rhizobia
ModelGenerator
FindModel
Model fitting in phylogenetics
Bayesian phylogenetics
An Introduction to Bayesian Phylogenetics by Mike Lee
Maximum likelihood
Maximum Likelihood in Phylogenetics by Paul Lewis
Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data by Paul Lewis
Phylogenetics, applications
Historical Biogeography
Caribbean Research Resources [Permit and travel info]
Island Biogeography [Arachnids of West Indies and Madagascar]
Software, programs, tools
Archaeopteryx [Visualization, Analysis, and Editing of Phylogenetic Trees]
BIO::Phylo
DendroPy Phylogenetic Computing Library
EvolView [easy-to-use tool for displaying, managing and customizing phylogenetic trees]
ExPASy - Bioinformatics Resources Portal
E.T.E [a Python Environment for phylogenetic Tree Exploration]
GenGIS [Link phylogenies and specimen/sequence data with digital maps]
iTOL-Interactive Tree Of Life [phylogeny and data visualization tool]
Jalview [interactive editing, analysis and visualization of multiple sequence alignments]
List of software/programs compiled by Joe Felsenstein
Pablo Vinuesa's collection of evolutionary genomics resour
PLUTo: Phyloinformatic Literature Unlocking Tools
Phylemon2 - Phylogenetic analyses online environment
Phylostatic!
phyloT - generate a phylogeny from NCBI taxonomy
PieTree - display ancestral states on a phylogeny with pie-
Shapesr-phylo.org [phylogenetic comparative methods wiki]
Sequence manipulation suite
SVAMP - Sequence Variation Analysis,Maps and Phylogeny
Treedyn [tree annotation and graphics]
Treegraph [graphical editor for phylogenetic trees]
T-REX [a web server for inferring, validating and visualizing phylogenetic trees and networks]
Phylab [Java applet for teaching phylogenetics] VoSeq [database for storing voucher and DNA sequences]
PhyloWidget [viewing, editing, and publishing phylogenetic trees online]PhyloXML [an XML language designed to describe phylogenetic trees]
Learning materials (courses, workshops)
2nd National Postgraduate Training Workshop in Systematics
ANU PhyloWorkshop [6 Lectures]
Bioinformatics Workshop and Training - List by Stephen Turner
Brown University BIO 1425 "Phylogenetic Biology" by Casey Dunn
DNA sequence based studies of microbial diversity (by Jonathan Eisen)
Current Topics in Phylogenetics [with tutorials on programs]
Essential Cladistics
Evolution and Genomics
Harvard "OEB 181: Systematics" (by Gonzalo Giribet & Charles Marshall)
Iowa State U. "Molecular Phylogenetics"
Kansas University "Phylogenetic Methods"
Kerstin Hoef-Emden - Introduction to Molecular Phylogeny [PDF]
NESCENT Academy
Phylogenetic Reconstruction [Evolution textbook chapter]
Phylogeography: Spatial Evolutionary Genetics (by A. Crawford)
Courses
BYU "Introduction to Phylogenetic Comparative Methods" (by Juan Santos)
Phylometh.org - online phylogenetics course by Brian O'meara
Principles of biological systematics and nomenclature
TAMU "Quantitative Phylogenetics" (by Mariana Mateos & Jim Woolley)
Texas Tech "Principles and Practice of Phylogenetic Systematics"
U. Alaska "Introduction to Biosystematics" (by Derek Sites)
U. Alaska "Systematics and Comparative Biology" (by Derek Sites)
U. Conn. Seminar in Comparative Biology
U. Conn. Phylogenetics (by Paul Lewis)
U. Idaho Principles of Systematic Biology (by Jack Sullivan)
U. Utah "Building Evolutionary Trees: Method, Theory & Controversy"
U. Washington "Phylogenetic Inference" (by Joe Felsenstein)
U. Wisconsin "Phylogenetic Analysis of Molecular Data" (David A. Baum)
Various Guides to Molecular Phylogenetics by Peter Unmack
Research labs and groups
Phylogenetics
Stockholm Phylogenomics Group
Zoological Systematics and Evolution, Barcelona, Spain Phylodiversity.net
Phylogenetics - applied research
SPSAS-evo
Beetles
Water and Cave Beetle Evolution Lab (Spain, CSIC)
Andrew Short's lab (aquatic beetles), Kansas University
Social media
Phylobabble [discussion forum for phylogenetic theory and applications]