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diff --git a/biology/phylip/pkg-descr b/biology/phylip/pkg-descr new file mode 100644 index 000000000000..34988635d2fb --- /dev/null +++ b/biology/phylip/pkg-descr @@ -0,0 +1,45 @@ + PHYLIP - Phylogeny Inference Package (version 3.5) + + This is a FREE package of programs for inferring phylogenies and carrying +out certain related tasks. At present it contains 30 programs, which carry out +different algorithms on different kinds of data. The programs in the package +are: + ---------- Programs for molecular sequence data ---------- + PROTPARS Protein parsimony DNAPARS Parsimony method for DNA + DNAMOVE Interactive DNA parsimony DNAPENNY Branch and bound for DNA + DNACOMP Compatibility for DNA DNAINVAR Phylogenetic invariants + DNAML Maximum likelihood method DNAMLK DNA ML with molecular clock + DNADIST Distances from sequences PROTDIST Distances from proteins + RESTML ML for restriction sites SEQBOOT Bootstraps sequence data sets + ----------- Programs for distance matrix data ------------ + FITCH Fitch-Margoliash and least-squares methods + KITSCH Fitch-Margoliash and least squares methods with evolutionary clock + NEIGHBOR Neighbor-joining and UPGMA methods + -------- Programs for gene frequencies and continuous characters ------- + CONTML Maximum likelihood method GENDIST Computes genetic distances + CONTRAST Computes contrasts and correlations for comparative method studies + ------------- Programs for 0-1 discrete state data ----------- + MIX Wagner, Camin-Sokal, and mixed parsimony criteria + MOVE Interactive Wagner, C-S, mixed parsimony program + PENNY Finds all most parsimonious trees by branch-and-bound + DOLLOP, DOLMOVE, DOLPENNY same as preceding four programs, but for + the Dollo and polymorphism parsimony criteria + CLIQUE Compatibility method FACTOR recode multistate characters + ---------- Programs for plotting trees and consensus trees ------- + DRAWGRAM Draws cladograms and phenograms on screens, plotters and printers + DRAWTREE Draws unrooted phylogenies on screens, plotters and printers + CONSENSE Majority-rule and strict consensus trees + RETREE Reroots, changes names and branch lengths, and flips trees + +There is also an Unsupported Division containing two programs, makeinf and +ProtML, which were contributed by others and are maintained by their authors. + +The package includes extensive documentation files that provide the information +necessary to use and modify the programs. + + Joe Felsenstein + joe@genetics.washington.edu + Department of Genetics + University of Washington + Box 357360 + Seattle, Washington 98195-7360, U.S.A. |