################## ## ## ## PHYLIP 3.4 ## ## ## ################## Welcome to version 3.4 of PHYLIP. This file describes the other files so that you know what you have received. The files are in the same order in the diskette, magnetic tape, and electronic network distributions of PHYLIP, and the source code files and documentation files are identical in all three versions. Note the convention used for naming files: a program named CONTML becomes file CONTML.PAS. The documentation file for each program has the same name as the program, followed by ".DOC" instead of ".PAS". Thus the documentation file for CONTML is CONTML.DOC. Documentation files for groups of programs also have ".DOC" endings, for example the discrete characters programs documentation file is DISCRETE.DOC. Below is a table of the order and names of the files. The documentation files and programs consist entirely of text, with one exception. At the end of every page of the each documentation file there is a form-feed character (in ASCII or ISO character codes this is a Control-L) which I hope will have the same effect on all printers -- to cause the page to be ejected. This is an attempt to compensate for the slight irregularity of page lengths. Unless you have ordered one of the precompiled versions, I have not provided you with compiled versions of these programs: it is up to you to get ahold of a compiler, modify the programs to work with that compiler (reading my documentation files and your compiler documentation carefully), and compile them. Please read the appropriate documentation files. Note the list-server news bulletins about the package that you can fetch or subscribe to by electronic mail, and note the precompiled versions for PCDOS systems and Apple Macintoshes. I would appreciate hearing from you about any incompatibilities you encounter that are not already mentioned in the main documentation file MAIN.DOC. CONTENTS OF THE PACKAGE The package contains 75 files. In the electronic mail version some of these files may be split into parts, so there may be more. The package is organized hierarchically, with each file or group of files preceded by its documentation file: Files Contents ---- -------- 1 this READ.ME file describing the contents of the package 2 the general documentation file 3 documentation for molecular sequence programs 4 documentation for PROTPARS 5 PROTPARS -- Parsimony for protein sequence data 6 documentation for DNAPARS 7 DNAPARS -- DNA parsimony program 8 documentation for DNAMOVE 9 DNAMOVE -- interactive DNA parsimony 10 documentation for DNAPENNY 11 DNAPENNY -- Branch and bound method for DNA 12 documentation for DNABOOT 13 DNABOOT -- Bootstrap of DNA parsimony method 14 documentation for DNACOMP 15 DNACOMP -- DNA compatibility program 16 documentation for DNAINVAR 17 DNAINVAR -- computation of Lake's and Cavender's invariants 18 documentation for DNAML 19 DNAML -- DNA maximum likelihood program 20 documentation for DNAMLK 21 DNAMLK -- DNA maximum likelihood with molecular clock 22 documentation for DNADIST 23 DNADIST -- Computes distance matrix from sequences 24 documentation for RESTML 25 RESTML -- Maximum likelihood for restriction sites 26 documentation for SEQBOOT 27 SEQBOOT -- Makes multiple data sets by bootstrap resampling 28 documentation for distance matrix programs 29 documentation for FITCH 30 FITCH -- Fitch-Margoliash and least-squares methods 31 documentation for KITSCH 32 KITSCH -- F-M, L-S methods with evolutionary clock 33 documentation for NEIGHBOR 34 NEIGHBOR -- Neighbor joining and UPGMA methods 35 documentation for gene frequency, continuous character programs 36 documentation for CONTML 37 CONTML -- maximum likelihood program 38 documentation for GENDIST 39 GENDIST -- computes genetic distances 40 documentation for CONTRAST 41 CONTRAST -- Contrasts etc. for comparative method studies 42 documentation for discrete character programs 43 documentation for MIX 44 MIX -- both Wagner and Camin-Sokal parsimony and mixtures 45 documentation for MOVE 46 MOVE -- interactive Wagner, Camin-Sokal and mixed parsimony 47 documentation for PENNY 48 PENNY -- finds all most parsimonious trees 49 documentation for BOOT 50 BOOT -- Bootstrap confidence interval on MIX methods 51 documentation for DOLLOP 52 DOLLOP -- Dollo and polymorphism parsimony methods 53 documentation for DOLMOVE 54 DOLMOVE -- interactive Dollo and polymorphism parsimony 55 documentation for DOLPENNY 56 DOLPENNY -- Branch and bound for Dollo, polymorphism 57 documentation for DOLBOOT 58 DOLBOOT -- Bootstrap on Dollo and polymorphism methods 59 documentation for CLIQUE 60 CLIQUE -- compatibility program 61 documentation for FACTOR 62 FACTOR -- recode multistate to binary characters 63 documentation for tree plotting programs 64 documentation for DRAWGRAM 65 DRAWGRAM -- makes plots of cladograms, phenograms 66 documentation for DRAWTREE 67 DRAWTREE -- makes plots of unrooted phylogenies 68 FONT1 -- digitized font (simple Roman) 69 FONT2 -- digitized font (medium quality Roman) 70 FONT3 -- digitized font (high quality Roman) 71 FONT4 -- digitized font (medium quality Italic) 72 FONT5 -- digitized font (high quality Italic) 73 FONT6 -- digitized font (Russian Cyrillic) 74 documentation for consensus tree program 75 CONSENSE -- Majority-rule and strict consensus trees