PHYLIP
Phylip is a suite of phylogeny programs.
Contents |
[edit] 1 Available Console Commands
[edit] 1.1 Molecular sequence methods
- protpars: protein parsimony
- dnapars: DNA sequence
- dnapenny: DNA parsimony branch and bound
- dnamove: interactive DNA parsimony
- dnaml: DNA maximum likelihood
- dnamlk: DNA maximum likelihood with clock
- proml: Protein sequence maximum likelihood
- promlk: Protein sequence maximum likelihood
- dnainvar: DNA invariants
- dnadist: DNA distance
- protdist: Protein sequence distance
- restdist: Restriction sites and fragments distances
- restml: Restriction sites maximum likelihood
- seqboot: Bootstrapping/Jackknifing
[edit] 1.2 Distance matrix methods
- fitch: Fitch-Margoliash distance matrix method
- kitsch: Fitch-Margoliash distance matrix with clock
- neighbor: Neighbor-Joining and UPGMA method
[edit] 1.3 Gene frequencies and continuous characters
- contml: Maximum likelihood continuous characters and gene frequencies
- contrast: Contrast method
- gendist: Genetic distance
[edit] 1.4 Discrete characters methods
- pars: Unordered multistate parsimony
- mix: Mixed method parsimony
- penny: Branch and bound mixed method parsimony
- move: Interactive mixed method parsimony
- dollop: Dollo and polymorphism parsimony
- dolpenny: Dollo and polymorphism branch and bound parsimony
- dolmove: Dollo and polymorphism interactive parsimony
- clique: 0/1 characters compatibility method
- factor: Character recoding