PHYLIP

Joe Felseinstein

DNA and RNA sequence data

DNAPARS. Estimates phylogenies by the parsimony method using nucleic acid sequences. Allows use the full IUB ambiguity codes, and estimates ancestral nucleotide states. Gaps treated as a fifth nucleotide state.

DNAMOVE. Interactive construction of phylogenies from nucleic acid sequences, with their evaluation by parsimony and compatibility and the display of reconstructed ancestral bases. This can be used to find parsimony or compatibility estimates by hand.

DNAPENNY. Finds all most parsimonious phylogenies for nucleic acid sequences by branch-and-bound search. This may not be practical (depending on the data) for more than 10 or 11 species.

DNACOMP. Estimates phylogenies from nucleic acid sequence data using the compatibility criterion, which searches for the largest number of sites which could have all states (nucleotides) uniquely evolved on the same tree. Compatibility is particularly appropriate when sites vary greatly in their rates of evolution, but we do not know in advance which are the less reliable ones.

DNAINVAR. For nucleic acid sequence data on four species, computes Lake's and Cavender's phylogenetic invariants, which test alternative tree topologies. The program also tabulates the frequencies of occurrence of the different nucleotide patterns. Lake's invariants are the method which he calls "evolutionary parsimony".

DNAML. Estimates phylogenies from nucleotide sequences by maximum likelihood. The model employed allows for unequal expected frequencies of the four nucleotides, for unequal rates of transitions and transversions, and for different (prespecified) rates of change in different categories of sites, with the program inferring which sites have which rates.

DNAMLK. Same as DNAML but assumes a molecular clock. The use of the two programs together permits a likelihood ratio test of the molecular clock hypothesis to be made.

DNADIST. Computes four different distances between species from nucleic acid sequences. The distances can then be used in the distance matrix programs. The distances are the Jukes-Cantor formula, one based on Kimura's 2- parameter method, Jin and Nei's distance which allows for rate variation from site to site, and a maximum likelihood method using the model employed in DNAML. The latter method of computing distances can be very slow. (See the Distance Matrix programs pages for information on them).

SEQBOOT. Reads in a data set, and produces multiple data sets from it by bootstrap resampling. Since most programs in the current version of the package allow processing of multiple data sets, this can be used together with the consensus tree program CONSENSE to do bootstrap (or delete-half-jackknife) analyses with most of the methods in this package. This program also allows the Archie/Faith technique of permutation of species within characters.

CONSENSE. Computes consensus trees by the majority-rule consensus tree method, which also allows one to easily find the strict consensus tree. Does NOT compute the Adams consensus tree. Trees are input in a tree file in standard nested-parenthesis notation, which is produced by many of the tree estimation programs in the package. This program can be used as the final step in doing bootstrap analyses for many of the methods in the package.

protein sequences

PROTPARS. Estimates phylogenies from protein sequences (input using the standard one-letter code for amino acids) using the parsimony method, in a variant which counts only those nucleotide changes that change the amino acid, on the assumption that silent changes are more easily accomplished.

PROTDIST. Computes a distance measure for protein sequences, using maximum likelihood estimates based on the Dayhoff PAM matrix, Kimura's 1983 approximation to it, or a model based on the genetic code plus a constraint on changing to a different category of amino acid. The distances can then be used in the distance matrix programs.

SEQBOOT. Reads in a data set, and produces multiple data sets from it by bootstrap resampling. Since most programs in the current version of the package allow processing of multiple data sets, this can be used together with the consensus tree program CONSENSE to do bootstrap (or delete-half-jackknife) analyses with most of the methods in this package. This program also allows the Archie/Faith technique of permutation of species within characters.

CONSENSE. Computes consensus trees by the majority-rule consensus tree method, which also allows one to easily find the strict consensus tree. Does NOT compute the Adams consensus tree. Trees are input in a tree file in standard nested-parenthesis notation, which is produced by many of the tree estimation programs in the package. This program can be used as the final step in doing bootstrap analyses for many of the methods in the package.

distance matrix data

FITCH. Estimates phylogenies from distance matrix data under the "additive tree model" according to which the distances are expected to equal the sums of branch lengths between the species. Uses the Fitch-Margoliash criterion and some related least squares criteria. Does not assume an evolutionary clock. This program will be useful with distances computed from DNA sequences, with DNA hybridization measurements, and with genetic distances computed from gene frequencies.

KITSCH. Estimates phylogenies from distance matrix data under the "ultrametric" model which is the same as the additive tree model except that an evolutionary clock is assumed. The Fitch-Margoliash criterion and other least squares criteria are assumed. This program will be useful with distances computes from DNA sequences, with DNA hybridization measurements, and with genetic distances computed from gene frequencies.

NEIGHBOR. An implementation by Mary Kuhner and John Yamato of Saitou and Nei's "Neighbor Joining Method," and of the UPGMA (Average Linkage clustering) method. Neighbor Joining is a distance matrix method producing an unrooted tree without the assumption of a clock. UPGMA does assume a clock. The branch lengths are not optimized by the least squares criterion but the methods are very fast and thus can handle much larger data sets.

Tree manipulation, plotting, consensus

DRAWGRAM. Plots rooted phylogenies, cladograms, and phenograms in a wide variety of user-controllable formats. The program is interactive and allows previewing of the tree on PC graphics screens, and Tektronix or DEC graphics terminals. Final output can be on a laser printer (such as the Apple Laserwriter or HP Laserjet), on graphics screens or terminals, in files readable by drawing programs such as PC Paintbrush, MacDraw, Idraw, and Xfig, on pen plotters (Hewlett-Packard or Houston Instruments) or on dot matrix printers capable of graphics. Select here to see a sample plot.

DRAWTREE. Similar to DRAWGRAM but plots unrooted phylogenies. Select here to see a sample plot.

CONSENSE. Computes consensus trees by the majority-rule consensus tree method, which also allows one to easily find the strict consensus tree. Does NOT compute the Adams consensus tree. Trees are input in a tree file in standard nested-parenthesis notation, which is produced by many of the tree estimation programs in the package. This program can be used as the final step in doing bootstrap analyses for many of the methods in the package.

RETREE. Reads in a tree (with branch lengths if necessary) and allows you to reroot the tree, to flip branches, to change species names and branch lengths, and then write the result out. Can be used to convert between rooted and unrooted trees.