Package: PHYLIP
PHYLIP - Package for Inferring Phylogenies
Documentation
Main Phylip documentation file
$doc/Phylip/main.html
Continuous character programs
$doc/Phylip/contchar.html
Discrete (0,1) character programs
$doc/Phylip/discrete.html
Distance matrix programs
$doc/Phylip/distance.html
Tree drawing programs
$doc/Phylip/draw.html
Sequence phylogeny programs
$doc/Phylip/sequence.html
Web site
https://phylipweb.github.io/phylip/
Git Development Site
https://github.com/felsenst/phylip
Data
Platforms
:
solaris-sparc, linux-intel, solaris-amd64, linux-x86_64, osx-x86_64
Installation
:
BIRCH
Programs
:
clique - Compatability method for two-state characters
consense - Consensus trees
contml - Gene Frequencies and Continuous Characters Maximum Likelihood
contrast - compute contrasts for comparative method
dnacomp - DNA phylogeny using compatability method
dnadist - Construct distance matrix for DNA sequences
dnainvar - DNA sequence phylogeny invariants
dnaml - DNA phylogeny using Maximum Likelihood
dnamlk - DNA phylogeny using Maximum Likelihood (with evolutionary clock)
dnamove - DNA parsimony with interactive tree rearrangement
dnapars - DNA parsimony
dnapenny - DNA parsimony using branch and bound method
dollop - Discrete data parsimony method of DOLLO
dolmove - Interactive Dollo and Polymorphism Parsimony
dolpenny - Branch and bound parsimony using Dollo and polymorphism methods
drawgram - Draw cladograms
drawtree - Draw radial trees
factor - Generate discrete (0,1) characters from multistate characters
fitch - Distance trees - Fitch/ Margoliash
gendist - Compute genetic distances from gene frequencies
kitsch - Distance trees - Fitch/ Margoliash (molecular clock)
mix - Mixed method discrete character parsimony
move - Interactive mixed-method parsimony
neighbor - Distance trees - Neighbor-Joining/UPGMA
pars - Discrete character parsimony
penny - Branch and bound parsimony for discrete data
proml - protein phylogeny using maximum likelihood
promlk - protein phylogeny by maximum likelihood, constant evolutionary clock
protdist - Construct distance matrix for protein sequences
protpars - Protein parsimony
restdist - Compute distance matrices for discrete data
restml - Maximum likelihood phylogeny for discrete data
retree - Rearrange and reroot phylogenetic trees
seqboot - Create resampled datasets
treedist - Calculate distance between trees