Applied Bioinformatics Course

List of phylogeney programs

• Phylogeny software - The whole list of phylogeny programs collected and classified in groups by Joe Felsenstein.

Online phylogeney servers

• WebLab Protocols - The WebLab platform we develop and maintain has integrated the Phylip package. The protocols and macros for both Neighbor Joining and maximum parsimony methods are extremely useful for biologists to construct phylogeny trees with well defined data sets.
• NUS EMBOSS interface - The web interface of the Phylip programs integrated in the EMBOSS package, maintained by University of Singapore.
• EBC interface - The web interface of some Phylip programs, maintained by Uppsala University, Sweden.

Phylogeny programs

• Phylip - The web site for the comprehensive package Phylogeny Inference Package (Phylip) created and maintained by Joe Felsenstein at the University of Washington. This package can be downloaded and installed on Linux, Windows and Mac freely.
• Tree-Puzzle - The web page for the phylogeny program which uses the maximum likelihood method to analogize nucleotide and amino acid sequences as well as other two-state data.
• PAML - The web site for the Phylogenetic Analysis by Maximum Likelihood package developed and maintained by Ziheng Yang, at University College, London.
• MEGA - The web site for the Molecular Evolutionary Genetics Analysis package developed and maintained by Masatoshi Nei and his colleagues. It was originally designed for the Windows platform with a graphics interface and uses the distance method to construct phylogenetic trees. [PDF]

Display of phylogenetic trees

• iTOL - The web site of Interactive Tree of Life for the display and manipulation of phylogenetic trees, developed and maintained by the European Molecular Biology Laboratory.