The source code and documentation of the package consists of 89 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 -- describes the contents of the package
2 main.doc -- this 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 VMS command file to compile all of PHYLIP
8 vaxfix.c -- procedures needed to fix 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 coallike.c -- coalescent likelihoods from sampled phylogenies
25 fitch.c -- Fitch-Margoliash and least-squares methods
26 kitsch.c -- F-M, L-S methods with evolutionary clock
27 neighbor.c -- neighbor-joining and UPGMA methods
28 contml.c -- maximum likelihood program
29 gendist.c -- computes genetic distances
30 contrast.c -- contrasts etc. for comparative method studies
31 mix.c -- Wagner, Camin-Sokal parsimony and mixtures, part 1
32 mix2.c -- Wagner, Camin-Sokal parsimony and mixtures, part 2
33 move.c -- interactive Wagner, Camin-Sokal and mixed parsimony
34 penny.c -- finds all most parsimonious trees
35 dollop.c -- Dollo and polymorphism parsimony methods
36 dolmove.c -- interactive Dollo and polymorphism parsimony
37 dolpenny.c -- branch and bound for Dollo, polymorphism
38 clique.c -- compatibility program
39 factor.c -- recode multistate to binary characters
40 drawgraphics.h -- header file for drawgraphics.c
41 drawgraphics.c -- routines used in both drawgram.c and drawtree.c
42 interface.h -- header for Mac interface
43 interface.c -- Mac routines used in Mac interface
44 drawgram.c -- makes plots of cladograms, phenograms
45 drawtree.c -- makes plots of unrooted phylogenies
46 font1 -- digitized font (simple sans-serif Roman)
47 font2 -- digitized font (medium quality sans-serif Roman)
48 font3 -- digitized font (high quality serifed Roman)
49 font4 -- digitized font (medium quality sans-serif Italic)
50 font5 -- digitized font (high quality serifed Italic)
51 font6 -- digitized font (Russian Cyrillic)
52 consense.c -- majority-rule and strict consensus trees
53 retree.c -- reroots, rearranges and changes lengths on trees
The Documentation
54 sequence.doc -- documentation for molecular sequence programs
55 protpars.doc -- documentation for protpars.c
56 dnapars.doc -- documentation for dnapars.c
57 dnamove.doc -- documentation for dnamove.c
58 dnapenny.doc -- documentation for dnapenny.c
59 dnacomp.doc -- documentation for dnacomp.c
60 dnainvar.doc -- documentation for dnainvar.c
61 dnaml.doc -- documentation for dnaml.c and dnaml2.c
62 dnamlk.doc -- documentation for dnamlk.c and dnamlk2.c
63 dnadist.doc -- documentation for dnadist.c
64 protdist.doc -- documentation for protdist.c
65 restml.doc -- documentation for restml.c and restml2.c
66 seqboot.doc -- documentation for seqboot.c
67 coallike.doc -- documentation for coallike.c
68 distance.doc -- documentation for distance matrix programs
69 fitch.doc -- documentation for fitch.c
70 kitsch.doc -- documentation for kitsch.c
71 neighbor.doc -- documentation for neighbor.c
72 contchar.doc -- documentation for gene frequency
and continuous character programs
73 contml.doc -- documentation for contml.c
74 gendist.doc -- documentation for gendist.c
75 contrast.doc -- documentation for contrast.c
76 discrete.doc -- documentation for discrete character programs
77 mix.doc -- documentation for mix.c
78 move.doc -- documentation for move.c
79 penny.doc -- documentation for penny.c
80 dollop.doc -- documentation for dollop.c
81 dolmove.doc -- documentation for dolmove.c
82 dolpenny.doc -- documentation for dolpenny.c
83 clique.doc -- documentation for clique.c
84 factor.doc -- documentation for factor.c
85 draw.doc -- documentation for tree plotting programs
86 drawgram.doc -- documentation for drawgram.c
87 drawtree.doc -- documentation for drawtree.c
88 consense.doc -- documentation for consense.c
89 retree.doc -- documentation for retree.c
The Unsupported Division
90 makeinf.doc -- documentation for makeinf (by Arend Sidow)
91 makeinf.c -- C source for makeinf
92 protml.doc -- documentation for ProtML (by Adachi and Hasegawa)
93 protml.pas -- Pascal source for ProtML
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Maintained 15 Jul 1996 -- by Martin Hilbers(e-mail:M.P.Hilbers@dl.ac.uk)