FAQ (Frequently Asked Questions) at Phylip Home Page

DNA and RNA Sequences

• dnapars: Estimates phylogenies by the parsimony method using nucleic acid sequences.
  • Allows use of all IUB ambiguity codes, and estimates ancestral nucleotide states. Gaps treated as a fifth nucleotide state.
• dnadist: Computes four different distances between species from nucleic acid sequences. The distances can be used in the distance matrix programs. The distances are:
  • Jukes-Cantor distance
  • Kimura's 2-parameter distance
  • Jin and Nei's distance (which allows for rate variation from site to site)
  • a maximum likelihood method using the model employed in dnaml
  Note that the maximum likelihood method of computing distances can be very slow.

Protein sequences

• protpars: Estimates phylogenies from protein sequences using the parsimony method.
  • It uses 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.
  • The measure is 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 be used in the distance matrix programs.

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 (the same as the additive tree model except it assumes an evolutionary clock).
  • 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: Saitou and Nei's neighbor-joining method and the UPGMA method (Unweighted Pair Group Method with Arithmetic Mean).
  • 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.
  • Implemented by Mary Kuhner and John Yamato.

Discrete two-state (0,1) characters

• mix: Estimates phylogenies using parsimony for discrete character data with two states (0 and 1).
  • Allows use of the Wagner parsimony method, the Camin-Sokal parsimony method, or arbitrary mixtures of these.
  • Reconstructs ancestral states and allows weighting of characters.
• clique: Finds the largest clique of mutually compatible characters, and the phylogeny which they recommend, for discrete character data with two states.
  • The largest clique (or all cliques within a given size range of the largest one) are found by a very fast branch-and-bound search method.
  • The method does not allow for missing data. For such cases, the T (Threshold) option of mix may be a useful alternative.
  • Compatibility methods are particular useful when some characters are of poor quality and the rest of good quality, but when it is not known in advance which ones are which.

Bootstrapping

• 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.

Make consensus trees

• 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.

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