Useful links
General
Phylogenetic Programs
This is a small subset of available phylogenetic programs. If you are looking for more programs/options try this list compiled by Joseph Felsenstein.
Main phylogenetic programs we will use in class
- MAFFT sequence alignment
- FigTree drawing phylogenetic trees
- PAUP* Phylogenetic Analysis Using Parsimony PAUP
- TNT for a parsimony analysis
- PHYLIP, for various analysis and some obscure methods
- FastME distance analysis
- RAxML-NG Maximum Likelihood analysis
- IQ-TREE
- MrBayes Bayesian analysis
- PAML hypothesis testing
- Beast2 molecular clock analysis
- BayesTraits comparative studies
Other programs that can be useful
- Clustal (Omega, W and X) alternative MSA programs
- readAI conversion among various MSA formats
- TrimAI selecting most reliable positions in an MSA
- Gblocks an older program for removing poorly aligned regions of MSA
- PHYML for a simple ML analysis
- PhyloBayes & Coevol for a fancy Bayesian analysis
- RevBayes Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language
- Dendroscope an alternative program for drawing phylogenetic trees
- iTOL an online tool for the display, annotation and management of phylogenetic trees
- Mesquite
- TRACER analyzing Bayesian output
- Seq-Gen simulate sequence evolution on a phylogeny
Systematics/Phylogenetics Sites
Blogs
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