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