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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% %%
%% PHYLIP (Phylogeny Inference Package) Version 3.5c %%
%% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
COPYRIGHT NOTICE
(c) Copyright 1986-1995 by Joseph Felsenstein and the University of Washington.
Permission is granted to copy this document provided that no fee is charged for
it and that this copyright notice is not removed.
CONTENTS OF THIS PACKAGE
The source code and documentation of the package consists of 87 files,
plus 4 more for the programs in the Unsupported Division. In the electronic
mail version some of these files may be split into parts, so there may be more.
The package is organized into three major parts, the source code, the
documentation, and the unsupported programs. The documentation is organized
hierarchically, with groups of documentation files for different kinds of data
each preceded by a documentation file for the group as well. The "unsupported
division" of PHYLIP contains programs contributed by others (and not supported
by us) that we feel may of use to you.
Files Contents
---- --------
1 README -- this description of the contents of the package
2 main.doc -- the general documentation file
The Source code
3 Makefile -- the "Makefile" to be used by C's that have "make"
4 Makefile.qc -- the Makefile for Microsoft C and Quick C
5 Makefile.tc -- the Makefile for Borland Turbo C and Borland C
6 phylip.h -- the PHYLIP "header file"
7 compile.com -- a VAX VMS command file to compile all of PHYLIP
8 vaxfix.c -- procedures needed to fix VAX VMS printf(" %hd ")
9 protpars.c -- parsimony for protein sequence data
10 dnapars.c -- DNA parsimony program
11 dnamove.c -- interactive DNA parsimony
12 dnapenny.c -- branch and bound method for DNA
13 dnacomp.c -- DNA compatibility program
14 dnainvar.c -- computation of Lake's and Cavender's invariants
15 dnaml.c -- DNA maximum likelihood program, part 1
16 dnaml2.c -- DNA maximum likelihood program, part 2
17 dnamlk.c -- DNA maximum likelihood with molecular clock
18 dnamlk2.c -- DNA maximum likelihood with clock, part 2
19 dnadist.c -- computes distance matrix from sequences
20 protdist.c -- computes distance matrix from sequences
21 restml.c -- maximum likelihood for restriction sites
22 restml2.c -- maximum likelihood for restriction sites, part 2
23 seqboot.c -- makes multiple data sets by bootstrap resampling
24 fitch.c -- Fitch-Margoliash and least-squares methods
25 kitsch.c -- F-M, L-S methods with evolutionary clock
26 neighbor.c -- neighbor-joining and UPGMA methods
27 contml.c -- maximum likelihood program
28 gendist.c -- computes genetic distances
29 contrast.c -- contrasts etc. for comparative method studies
30 mix.c -- Wagner, Camin-Sokal parsimony and mixtures, part 1
31 mix2.c -- Wagner, Camin-Sokal parsimony and mixtures, part 2
32 move.c -- interactive Wagner, Camin-Sokal and mixed parsimony
33 penny.c -- finds all most parsimonious trees
34 dollop.c -- Dollo and polymorphism parsimony methods
35 dolmove.c -- interactive Dollo and polymorphism parsimony
36 dolpenny.c -- branch and bound for Dollo, polymorphism
37 clique.c -- compatibility program
38 factor.c -- recode multistate to binary characters
39 drawgraphics.h -- header file for drawgraphics.c
40 drawgraphics.c -- routines used in both drawgram.c and drawtree.c
41 interface.h -- header for Mac interface
42 interface.c -- Mac routines used in Mac interface
43 drawgram.c -- makes plots of cladograms, phenograms
44 drawtree.c -- makes plots of unrooted phylogenies
45 font1 -- digitized font (simple sans-serif Roman)
46 font2 -- digitized font (medium quality sans-serif Roman)
47 font3 -- digitized font (high quality serifed Roman)
48 font4 -- digitized font (medium quality sans-serif Italic)
49 font5 -- digitized font (high quality serifed Italic)
50 font6 -- digitized font (Russian Cyrillic)
51 consense.c -- majority-rule and strict consensus trees
52 retree.c -- reroots, rearranges and changes lengths on trees
The Documentation
53 sequence.doc -- documentation for molecular sequence programs
54 protpars.doc -- documentation for protpars.c
55 dnapars.doc -- documentation for dnapars.c
56 dnamove.doc -- documentation for dnamove.c
57 dnapenny.doc -- documentation for dnapenny.c
58 dnacomp.doc -- documentation for dnacomp.c
59 dnainvar.doc -- documentation for dnainvar.c
60 dnaml.doc -- documentation for dnaml.c and dnaml2.c
61 dnamlk.doc -- documentation for dnamlk.c and dnamlk2.c
62 dnadist.doc -- documentation for dnadist.c
63 protdist.doc -- documentation for protdist.c
64 restml.doc -- documentation for restml.c and restml2.c
65 seqboot.doc -- documentation for seqboot.c
66 distance.doc -- documentation for distance matrix programs
67 fitch.doc -- documentation for fitch.c
68 kitsch.doc -- documentation for kitsch.c
69 neighbor.doc -- documentation for neighbor.c
70 contchar.doc -- documentation for gene frequency
and continuous character programs
71 contml.doc -- documentation for contml.c
72 gendist.doc -- documentation for gendist.c
73 contrast.doc -- documentation for contrast.c
74 discrete.doc -- documentation for discrete character programs
75 mix.doc -- documentation for mix.c
76 move.doc -- documentation for move.c
77 penny.doc -- documentation for penny.c
78 dollop.doc -- documentation for dollop.c
79 dolmove.doc -- documentation for dolmove.c
80 dolpenny.doc -- documentation for dolpenny.c
81 clique.doc -- documentation for clique.c
82 factor.doc -- documentation for factor.c
83 draw.doc -- documentation for tree plotting programs
84 drawgram.doc -- documentation for drawgram.c
85 drawtree.doc -- documentation for drawtree.c
86 consense.doc -- documentation for consense.c
87 retree.doc -- documentation for retree.c
The Unsupported Division
88 makeinf.doc -- documentation for makeinf (by Arend Sidow)
89 makeinf.c -- C source for makeinf
90 protml.doc -- documentation for ProtML (by Adachi and Hasegawa)
91 protml.pas -- Pascal source for ProtML
Before using any of the programs you should read the main documentation
file main.doc, the documentation file for that group of programs, and
the documentation file for the program.
Joe Felsenstein
Electronic mail address (Internet): joe@genetics.washington.edu
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