Phylogeny

• Parsimony method programs
• Distance matrix method programs
• Maximum likelihood method programs
• Computation of distance
• Manipulation and visualization of phylogenetic tree
• Other programs

• Parsimony method programs

PHYLIP

• dnapars: Nucleic sequences.
• protpars: Protein sequences.
• pars: Discrete character parsimony
• mix: Mixed method parsimony.
• dollop: Dollo and Polymorphism Parsimony program.




LVB

• lvb: Reconstructing evolution with parsimony and simulated annealing.

• Computation of distance

PHYLIP

• dnadist: Aligned nucleic sequences.
• protdist: Aligned protein sequences.

EMBOSS

• distmat: Creates a distance matrix from multiple alignments

• Distance matrix method programs

PHYLIP

• neighbor: Neighbor-joining or UPGMA.
• fitch: Fitch-Margoliash and least-squares methods.
• kitsch: Fitch-Margoliash and least-squares methods with molecular clock.




BIONJ

• bionj: A version of the Neighbor Joining algorithm improved for molecular sequences.




WEIGHBOR

• weighbor: Weighted neighbor joining.




QUICKTREE

• quicktree: Rapid reconstruction of phylogenies by the Neighbor-Joining method.

• Maximum likelihood method programs

FASTDNAML

• FASTDNAML: Construction of phylogenetic trees of DNA sequences using maximum likelihood.




PHYML

• PHYML: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.




PUZZLE

• puzzle: Tree reconstruction for sequence data by maximum likelihood analysis and quartet puzzling.




SEQ-GEN

• seqgen: Sequence-Generator: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees.

• Manipulation and visualization of phylogenetic tree

PHYLIP

• drawtree: Draw a tree.
• drawgram: Draw a cladogram or a phénogram.
• consense: Consensus tree program.
• unroot: Unroot a tree with the retree program.




RBVOTREE

• rbvotree: Report bootstrap values found with Phylip consense program on tree found with Neighbor joining or UPGMA algorithm.

• Other programs

PHYLIP

• clique: Compatibility Program.




TREEALIGN

• treealign: A Unified Approach to Alignments and Phylogenies.




BAMBE

• bambe: Bayesian Analysis in Molecular Biology and Evolution.




TIPDATE

• tipdate: Analysis of trees with dated tips.