Phylogeny Resources
- Phylogenetics Factsheet
- Phylogenetic trees – tools for creation and visualization
- A beginner's guide to making a phylogenetic tree
- Interpreting and Estimating Phylogenies
- Trees and Tree - softwares for visualisation and manipulations: Dealing with phylogenetic trees - a "comprehensive list"
- PLoS Currents: new section on phylogenetic analyses (PLoS Currents: Tree of Life)
- NESCent (National Evolutionary Synthesis Center) Informatics Wiki NESCent's Informatics Program
- Phyloinformatics Summer of Code 2011
Phylogeny Programs
- A list of Phylogeny programs
- TreeFinder
- PhyML 3.0: new algorithms, methods and utilities
- MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences
- TREE-PUZZLE: Maximum likelihood analysis for nucleotide, amino acid, and two-state data
- DAMBE
- NONA
- TNT (TNT)
- Generate Phylogenetic Tree ViPR: Virus Pathogen Resource
- TreeSoft: Softwares for Phylogenetic Trees (TreeBeST Manual)
- PhyloWidget (Article: PhyloWidget: web-based visualizations for the tree of life)
Phylogenetic trees
- A Phylogeny of Complete Genomes: Data Repository (Tree of Life)
- The Newick tree format
Courses
- Genome 570: Phylogenetic Inference (Spring, 2008) @ University of Washington
- Genome 570: Phylogenetic Inference (Winter, 2010) @ University of Washington
- Zoology 304: Evolution
Books
- The phylogenetic handbook: A Practical Approach to phylogenetic analysis and hypothesis testing
Workshops
- Computational phyloinformatics
- Workshop on molecular evolution (molecularevolution{dot}org)
- Bodega Applied Phylogenetics Workshop
- Computational Phyloinformatics: A BGI-Shenzhen and NESCent Course5 August - 17 August 2010
- PHYLOINF09
Computational Phyloinformatics - a GTPB-NESCent Collaboration
Ensembl Resources
- Gene/Protein Tree
- Gene Orthology/Paralogy prediction method
- Article: EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
- Family and GeneTree stable ID in Compara
- ftp: Ensembl species list
- Ensembl: Help & Documentation
- Ensembl Help: Comparative Genomics
Articles
- A reference guide for tree analysis and visualization
- Visualization of multiple alignments, phylogenies and gene family evolution
- From gene trees to species trees II: Species tree inference in the deep coalescence model (2010)
- The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics
Cophylogeny
- Jane: a software tool for the cophylogeny reconstruction problem
RNA regulation
- The central role of RNA regulation in human development and cognition - John Mattick
Arena3D
- Arena3D: visualization of biological networks in 3D
