Building PHYLIP-3.57c with EMBOSS-2.9.0

I'm posting this here in the hope that it may save a bit of time and frustration for someone. This updated README (which actually contains the Installation instructions) for PHYLIP-3.573c clarifies a number of issues which are easy to miss if the instructions in the original README are followed.

Symptoms of these problems include the following error messages, obtained when one attempts to run the tools from the PHYLIP suite:


% ednadist
Error: File /usr/local/src/EMBOSS-2.9.0/embassy/phylip/emboss_acd/ednadist.acd line 0: ACD file not opened
%

This is caused by the absence of a directory 'phylip' - adding the symbolic link discussed in step 5) below fixes this problem.


% ednadist
Error: File /usr/share/EMBOSS/acd/ednadist.acd line 1: (ednadist) Attribute 'embassy' unknown
%

The root of this problem is a version mismatch in the ACD code for EMBOSS-2.9.0 and the PHYLIP-3.573c code. The problem is solved by re-compiling EMBOSS after applying a patch as discussed in step 6) of the updated README file below.




           %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
           %%                                                     %%
           %%  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 (at) genetics [.] washington [.] edu


	   Programs have now been modified to use the emboss command
language and sequence reading so programs expecting a standard phylip
sequence file can now use any sequence file format.
	 The interactive programs have not been modified or included
here as they would give no advantage form having an emboss interface.


Emboss problems mail emboss-bug (at) embnet [.] org


Installation.

This procedure assumes that EMBOSS has already been compiled and installed.
If this is not the case, obtain EMBOSS and install it following the
instructions provided with the EMBOSS package, taking care to apply
the patch discussed in step 6 below prior to compiling EMBOSS.

1) Go to the emboss source directory:

   cd EMBOSS-2.x.x

2) make new directory embassy if it does not exist already:

   mkdir embassy

3) Go into that directory:

   cd embassy

4) unzip and untar the file. N.B.: the resulting directory is called 
PHYLIP-3.57c, not PHYLIP-3.573c as one might expect.

   gunzip PHYLIP-3.573c.tar.gz
   tar xvf PHYLIP-3.573c.tar


5) create a symbolic link 'phylip' to the directory:

   ln -s phylip PHYLIP-3.573c.tar
    

6) replace the file EMBOSS-2.9.0/ajax/ajacd.c with a patched
version, which can be found at 
   
     ftp://ftp.uk.embnet.org/pub/EMBOSS/patchfiles/ajacd.c

7) recompile and re-install EMBOSS

8) go into the phylip directory

   cd PHYLIP-3.57c

9) configure and compile

   ./configure (use same options as you used to compile emboss)
   make
   make install

PureGin.org

Building PHYLIP-3.57c with EMBOSS-2.9.0

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