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paup

Larry_Goldstein at HGL-MAIL.HARVARD.EDU Larry_Goldstein at HGL-MAIL.HARVARD.EDU
Tue Oct 5 20:22:07 EST 1993


  
  In response to your letter received Tue, Oct 5, 1993 at 4:17 PM
  
  there are plenty of ibm based programs.  in fact i believe that paup was
  originally written for the ibm.  at any rate if you have gopher you can
access
  the software library at iubio in indiana.  they have quite a bit of
such
  software. 
  larry goldstein
  
       *     *     *     *     *
  
  Message-Id: <9310052220.AA29114 at net.bio.net>
  To: info-gcg at net.bio.net
  From: jenkins at uk.ac.nibsc.aidsun
  Subject: Phylogeny Software
  Date: 5 Oct 93 08:46:07 GMT
  Sender: list-admin at daresbury.ac.uk
  Precedence: first-class
  Original-To: info-gcg at uk.ac.daresbury
  
  
  
  ----- Begin Included Message -----
  
  I've had some indirect experience with the PAUP program
  (version 3.1) in making parsimony trees (viral).  
  I believe they are all Mac-based. I would like to try
  to obtain a similar program for IBM-PC/ MS-DOS.
  I would even be willing to pay for it ! :-(
  
  Is there such a thing, or will I have to get a Mac
  just for this one application?
  
  Thanks in advance.
  
  Brian
  
  
  ----- End Included Message -----
  
  There is a summary of phylogeny software written by Joe Felsenstein.  Here it
  is.
  
  
  
                         SOME AVAILABLE PHYLOGENY PROGRAMS
  
       The following material (except item 0) is  from  the  PHYLIP  version 
3.5
  documentation.   I  post  it  because it may be a useful compilation.  Here
are
  some of the phylogeny packages that I know about.  Some of them  are 
available
  over  Internet  from  ftp  server  machines.  If you are on Internet you
should
  familiarize yourself with ftp and with them (see entries 6 and 7 below for
more
  information).
                                 Table of Contents
  
        0. PHYLIP	             9. VOSTORG	             16. COMPROB
        1. PAUP	            10. MEGA	             17. MARKOV
        2. BIOSYS-1	    11. Evomony	             18. PHYSYS
        3. MacClade	    12. COMPONENT	     19. SINCAIDEN
        4. Hennig86	    13. Turbotree	     20. MUST
        5. ClaDOS	            14. Molevol   	     21. GDE
        6. TreeAlign	    15. CLINCH    	     22. TreeTool
        7. Clustal		
  
       0.  PHYLIP is a  free  package  of  programs  for  inferring 
phylogenies,
  including  programs  to  carry  out  parsimony, compatibility, distance
matrix,
  invariants ("evolutionary parsimony") and likelihood methods on  a  variety 
of
  different  kinds  of  data.   It is available in the recently-released
versions
  3.5c and 3.5p as C or Pascal source code and documentation, and in  four 
forms
  of  executables:  (i) for 386 and 486 systems under PCDOS, (ii) for 386 and
486
  systems under Windows, (iii) for non-386 and non-486 PCDOS  systems,  and 
(iv)
  for  Macintosh  systems.   The  C  source code will also compile easily on
most
  workstations  and  mainframes  that  have  a  C  compiler.    PHYLIP  has 
been
  distributed  by  me  since  1980, with over 2000 registered installations. 
New
  features  include  programs  to  compute   protein   sequence   distances,  
to
  interactively  modify  a  phylogeny,  and  to compute likelihoods in
coalescent
  models from samples of genealogies.  Most programs in the C version  no 
longer
  have  arbitrary  limits  on the numbers of sites of or species.  Many other
new
  features have been  added  as  well,  such  as  new  models  for  variation 
of
  evolutionary rates among sites in the DNA likelihood programs.
  
       PHYLIP      is      available      by       anonymous       ftp      
from
  evolution.genetics.washington.edu   (IP   number   128.95.12.41)  in 
directory
  pub/phylip.  Users who cannot get it this way can also  send  enough 
formatted
  diskettes,  which  will be returned with the particular form of the package
and
  its documentation written on them.  Contact me (preferably by electronic 
mail)
  for details of the diskette distribution or further information about anonymous
  ftp distribution.  The latest version of PHYLIP is  version  3.51  which 
fixes
  some bugs present in 3.5.
  
       1.  David Swofford of the Laboratory of  Molecular  Systematics, 
National
  Museum of Natural History, Smithsonian Instition, Washington, D.C.  has
written
  PAUP (Phylogenetic Analysis Using Parsimony).   It  can  be  ordered  from 
the
  Center  for  Biodiversity,  Illinois  Natural  History Survey, 607 East
Peabody
  Drive, Champaign, Illinois  61820, U.S.A.
  
       Since  December,  1985,  Swofford  has  been  distributing  a 
precompiled
  executable object-code versions of PAUP for the IBM PC and other MSDOS
systems.
  As of this writing (February, 1993) he has released version  3  (PAUP/Mac) 
for
  the  Macintosh,  and  later  hopes  to  release version 3 for PCDOS systems
and
  ultimately for mainframes.  The cost was $50, which will increase to $100
soon.
  Orders  received  for  the  Mac  version  will  be filled but the final
printed
  documentation will arrive later, as it is not completed yet.
  
       PAUP 3.0 is probably the most sophisticated parsimony program.  It 
allows
  multistate  characters,  user-defined  weights on individual state
transitions,
  Wagner,  Camin-Sokal  and  Dollo  parsimony   methods,   bootstrap  
confidence
  intervals,  and  finding  all  most parsimonious trees by branch-and-bound. 
It
  also has provision for computing Lake's linear phylogenetic  invariants.  
PAUP
  is (a great) many times faster than the parsimony programs in PHYLIP.
  
       2. Swofford also distributes  an  older  package  of  programs, 
BIOSYS-1,
  including some phylogeny estimation programs, for use with gene frequency
data,
  with particular attention to distance methods.  BIOSYS-1 is distributed  on 
an
  IBM PC-formatted floppy disk.  Included are precompiled versions for the IBM
PC
  and source code for uploading to IBM, VAX/VMS, Unix, Prime and  CDC 
mainframes
  and  minicomputers.   The  price  is  $25.00,  from  the  same address as
PAUP.
  BIOSYS-2 is under development, but it is too early to anticipate  a 
completion
  date.
  
       3.  If you have a Macintosh computer and any  interest  in 
discrete-state
  parsimony  methods (including DNA and protein parsimony), you should
definitely
  get MacClade.  It was written by Wayne  Maddison  and  David  Maddison  of 
the
  University  of  Arizona.  All distribution is by Sinauer Associates,
Sunderland
  Massachusetts 01375, USA.  Their phone number is: (413) 665  3722,  FAX: 
(413)
  665  7292.   A  disk with program, help file, and example data files, plus
book
  (which has about 100 pages of intro to phylogenetic theory, and  250  pages 
of
  program  instructions),  is  $75  U.S. ($40 for the book alone).  Site
licenses
  also available.   An earlier and less capable  Version  2  (which  for 
example
  cannot  read  nucleic  acid  sequences  and  has  fewer  features  for
discrete
  characters) is also available by anonymous  ftp  from  the  EMBL,  Indiana 
and
  Houston  molecular  biology  software servers.  Their addresses are given
below
  under the descriptions of TreeAlign and ClustalV.  MacClade 2.1 will  be 
found
  among their Mac software, as a squeezed and then binhexed file.
  
       MacClade enables you to use the  mouse-window  interface  to  specify 
and
  rearrange  phylogenies by hand, and watch the number of character steps and
the
  distribution of states of a given character on the tree change as  you  do 
so.
  MacClade  is  positively addictive and will give you a much better feel for
the
  tree and your data.  It's the closest thing to a phylogeny video  game  that 
I
  have  seen.   It  has been influential in spurring the inclusion of
interaction
  and graphics into other phylogeny programs.   (I  have  tried  to  supply 
this
  functionality  in  PHYLIP  by  incorporating  the  programs  MOVE, DOLMOVE,
and
  DNAMOVE,  which  act  somewhat  like  MacClade).   MacClade  does  not  have 
a
  sophisticated  search algorithm to find best trees: it largely relies on you
to
  do  it  by  hand  (which  is  surprisingly  effective),  with  only   a  
local
  rearrangement algorithm available to improve on that tree.
  
       4.  J. S. Farris has produced Hennig86, a fast parsimony program
including
  branch-and-bound  search  for  most  parsimonious  trees  and  interactive
tree
  rearrangement.  Although complete benchmarks have not been published it is
said
  to  be faster than Swofford's PAUP; both are a great many times faster than
the
  parsimony programs in PHYLIP.  The program is distributed in executable 
object
  code  only  and  costs $50, plus $5 mailing costs ($10 outside of of the
U.S.).
  The user's name should be  stated,  as  copies  are  personalized  as  a 
copy-
  protection  measure.   It  is  distributed  by  Arnold  Kluge,  Amphibians 
and
  Reptiles, Museum of  Zoology,  University  of  Michigan,  Ann  Arbor, 
Michigan
  48109-1079,  U.S.A.  It runs on PC-compatible microcomputers with at least
512K
  of RAM and needs no math coprocessor or graphics monitor.  It can handle up 
to
  180  taxa  and 999 characters.  An 80386 version, Hennig386, is currently
being
  tested but no release date has yet been announced.
  
       5. ClaDOS, an interactive program which allows rearrangement of trees 
and
  their  evaluation,  mapping of characters into them, and more, is available
for
  PCDOS systems from Kevin Nixon, L. H. Bailey Hortorium, Cornell University,
467
  Mann  Library,  Ithaca, New York  14853.  I have been unable to get
information
  on its cost or method of distribution.
  
       6. Jotun Hein, (Institute of Genetics and Ecology, University  of 
Aarhus,
  8000  Aarhus  C, Denmark) has produced TreeAlign, a multiple sequence
alignment
  program that builds trees as it aligns DNA or protein  sequences.   It  uses 
a
  combination  of  distance  matrix and approximate parsimony methods. 
TreeAlign
  uses too much memory for it to run on PC's (DOS or Mac systems) but  is 
really
  designed  for  a workstation or mainframe.  It is available by anonymous ftp
at
  the Indiana, Houston, and EMBL molecular biology software  distribution 
sites.
  Their    network    addresses    are    respectively:     
ftp.bio.indiana.edu,
  ftp.bchs.uh.edu, and ftp.embl-heidelberg.de.  In the Indiana archive  one 
must
  enter  directory  molbio/align,  in  the  Houston  archive  it  is in
directory
  pub/gene-server in the directories unix and vms, and on the EMBL archive it 
is
  in  pub/software/unix  and  pub/software/vax.   If  you are on Internet and
use
  molecular data it is important that you learn to use anonymous ftp  and 
become
  familiar with these ftp servers.
  
       7. Another multisequence alignment program  that  estimates  trees  as 
it
  aligns  multiple  sequences  is ClustalV.  An older version in PCDOS
executable
  form was distributed previously (see  below  for  information  on  how  to 
get
  executables  for  PC  or  Mac  for  the  current  version).   Currently  it 
is
  distributed as C source code by  its  author,  Desmond  Higgins.   Clustal 
was
  originally  developed  at  Trinity  College, Dublin, Ireland, but version V
was
  done at Higgin's current address, the European  Molecular  Biology 
Laboratory,
  Heidelberg,  Germany.   Clustal  V successfully compiles and runs on VAX/VMS
C,
  Apple  Macintosh  Think  C,  MSDOS  Turbo  C,  Decstation  ULTRIX   C,and  
Sun
  workstations  with  GNU C.  It is a complete rewrite and upgrade of the
Clustal
  package which was described by Higgins and Sharp (1989).
  
       New features include the ability to detect read  different  input 
formats
  (NBRF/  PIR, Fasta, EMBL/Swissprot); align old alignments; produce
phylogenetic
  trees after alignment (Neighbor Joining trees with a bootstrap  option); 
write
  different alignment formats (Clustal, NBRF/PIR, GCG, PHYLIP); full command
line
  interface.
  
       The program is available by anonymous ftp at  the  Indiana,  Houston, 
and
  EMBL  molecular  biology  distribution  sites.   Their  network  addresses 
are
  respectively: ftp.bio.indiana.edu, ftp.bchs.uh.edu, and ftp.embl-heidelberg.de.
  In the Indiana archive one must enter directory molbio/align,  in  the 
Houston
  archive  it is in directory pub/gene-server in all of the four directories
dos,
  Mac, unix, and vms, and on the EMBL  archive  it  is  in  pub/software/unix 
or
  pub/software/vax.   If  you  are  on  Internet  and  use  molecular  data it
is
  important  that  you learn to use anonymous ftp and become familiar with one
or
  more of these ftp servers.
  
       If you do not have any access to Internet, you could  alternatively 
start
  by sending e-mail to Des Higgins at:
            higgins at EMBL-Heidelberg.DE     (Internet)
  
       If you do not have access to e-mail, send a formatted PC or  MAC 
diskette
  (PLEASE state which) to:
       Des Higgins
       European Molecular Biology Laboratory
       Postfach 10.2209
       Meyerhofstrasse 1
       6900 Heidelberg
       Germany
  He will return the diskette with the source code  and  documentation.   He 
can
  also include an executable image for PC's or MAC.
  
       8. Gary Olsen, of the Department of Microbiology, University of 
Illinois,
  has  developed  a  speeded-up  version of my program DNAML coded in C, which
he
  calls "fastDNAml".  It achieves a number of economies and also is organized 
so
  that  it  can  be  run  on  parallel  processors  -- he and his co-workers
have
  constructed trees of very large size on a high-speed parallel  processor.  
The
  program  can  be  compiled using the "p4" portable parallel processing
toolkit.
  It can also be run in ordinary serial mode on workstations where it  is 
fatser
  than  DNAML.   The  C  program is available by anonymous ftp from the
Ribosomal
  Database Project at info.mcs.anl.gov in directory pub/RDP/programs/fastDNAml.
  
       9. Andrey A. Zharkikh,  Andrey  Rzhetsky,  and  their  co-workers  in 
the
  Institute  of  Cytology and Genetics, Siberian Branch of the Russian Academy
of
  Sciences, Novosibirsk, Russia, Ex-USSR, have produced  VOSTORG,  a  package 
of
  programs for alignment (both manual and automatic) and inferring phylogenies
by
  distance methods and parsimony for molecular sequences.  It  runs  on  IBM 
PC-
  compatibles and includes some rather fancy graphics.  The authors are
currently
  in the U.S., not in Siberia, and their program is sold for about $250 by
Exeter
  Software,  100  North  Country  Road, Setauket, NY 11733, USA.  Their
telephone
  number is 1-800-842-5892; Fax (516)751-3435.  The programs are described  in 
a
  paper by Zharkikh et. al. (1991).
  
       10. MEGA (Molecular Evolutionary Genetic Analysis) is due to  be 
released
  at the beginning of 1993 by Sudhir Kumar, Koichiro Tamura, and Masatoshi Nei
of
  the Institute of Molecular Evolutionary Genetics, 328 Mueller Lab,
Pennsylvania
  State  University,  University  Park, Pennsylvania 16802, U.S.A.  It will be
an
  executable program for PCDOS machines, and will be  menu-driven  with 
context-
  sensitive  help.  It will analyze data from DNA, RNA and protein sequences,
and
  distance matrices produced from other kinds of data as well.  It  will 
include
  the  Neighbor-Joining  method  distance  matrix  method,  a  branch  and 
bound
  parsimony method, and bootstrapping.  It will also plot trees on many kinds 
of
  printers.   The  program will be provided free of charge if you send one 1.2
Mb
  5.25-inch or 1.44 Mb 3.5-inch floppy diskette, and will be sent as soon  as 
it
  is  available.   Inquiries  can  also  be  made  by mail to M. Nei at the
above
  address or by electronic mail  to  nxm2 at psuvm  (Bitnet)  or 
nxm2 at psuvm.psu.edu
  (Internet).
  
       11.  James Lake will soon distribute "Evomony", a program  for  using 
the
  "evolutionary parsimony" (invariants) method for inferring phylogenies from
DNA
  or RNA sequences.  It runs on 286 and 386 PCDOS  systems  with  at  least 
500k
  bytes  of  memory.  Lake intends to distribute a PCDOS version by April 1,
1993
  (his choice of date, not mine!), with a Macintosh version to  follow  in 
1994.
  Both  will  be  distributed free to scientists in this field.  Exact
procedures
  for ordering Evomony have not yet been announced.  Lake's address is
Department
  of Biology, University of California, Los Angeles, California  90024.
  
       12.  Rod Page has written COMPONENT,  a  program  for  PCDOS  systems 
for
  comparing cladograms for use in phylogeny and biogeography studies.  It has
far
  more features for biogeographic studies (such as  comparing  species  and 
area
  cladograms)  than any other package.  It runs on PCDOS 286 or 386 systems
under
  Windows 3.0 or higher.   It will be released in the very near future.  Its
cost
  will  be  "in  the  $50-$75  range", and it can be ordered from Rod Page at
the
  Department of Botany, Natural History Museum, Cromwell Road,  London  SW7 
5BD,
  U.K.   His  phone and fax numbers are respectively (071)-938 9068 and 9260,
and
  his   e-mail   address   is   R.Page at natural-history-museum.imperial.ac.uk  
or
  rdp at nhm.ic.ac.uk.
  
       13.  David Penny (Department of Botany  and  Zoology,  Massey 
University,
  Palmerston  North, New Zealand) has been offering for free distribution
several
  PCDOS programs, one a fast parsimony program, TurboTree.  There  are  also 
two
  others,   Hadtree   which   computes   expected  frequencies  of  all 
possible
  distributions of nucleotides among species, and Great  Deluge,  an 
approximate
  search  for  the  most parsimonious tree by a quasi-random method.  He tells
me
  that funding exigiencies are such that he may soon have to start  charging 
for
  these.  His electronic mail address is dpenny at massey.ac.nz.
  
       14.   Walter  Fitch  (Department  of  Ecology  and  Evolutionary 
Biology,
  University  of  California,  Irvine,  California   92717, U.S.A.) has a
package
  "Molevol" available  free  (on  receipt  of  an  appropriate  number  of 
PCDOS
  formatted  floppy disks) with about 20 FORTRAN programs for not only
estimating
  trees by parsimony and distance methods but doing various  other 
manipulations
  of  data that might be needed such as format interconversions and searching
for
  homology and secondary structure.  They are available as FORTRAN source 
and/or
  as  PCDOS  executables.  The FORTRAN programs will also run on Sun
workstations
  (and probably others too, I would suspect).  His  electronic  mail  address 
is
  wfitch at daedalus.bio.uci.edu.
  
       15. Kent Fiala, now of SAS Institute, has written a compatibility
(clique)
  program,  based  on  an  earlier  program written by Kent and George
Estabrook.
  Christopher Meacham has put the latest version of  CLINCH  (6.2),  with 
Kent's
  permission, as a self-extracting DOS archive on Jim Beach's TAXACOM
fileserver,
  huh.harvard.edu,  for  anonymous   FTP.    The   self-extracting   archive  
is
  "CLINCH62.EXE"  in  directory  /pub/software/clinch.  This should be FTPed as
a
  binary file.  CLINCH62.EXE is about 150 kb.  When you run it, it will expand
to
  14  files  requiring  about  280  kb.   The  executable  program is
CLINCH.EXE.
  Readme, documentation, sample input and output, and  FORTRAN  source  code 
are
  included.   PC-CLINCH is probably the most sophisticated compatibility
analysis
  program.  The Taxacom server, by the way, also has other  material  related 
to
  botanical systematics, including flora information.
  
       16. Christopher Meacham (Department of Integrative Biology, University 
of
  California,  Berkeley,  California  94720,  U.S.A.)  produces COMPROB, a
Pascal
  program to compute probabilities that characters would be compatible at
random,
  thus  telling  us  which  clique  is  "most  surprising".   It is available
for
  anonymous ftp as a PCDOS executable from the Taxacom  server 
(huh.harvard.edu)
  in directory pub/mip.
  
       17.  The program MARKOV computes  a  distance  measure  between  pairs 
of
  nucleotide sequences.  It also constructs phylogenies from these and
summarizes
  the 4x4 substitution matrices between the pairs of species.   It  uses  a 
more
  general  model of substitution than used in PHYLIP, the Stationary Markov
Model
  described in the paper by Saccone et. al. in Methods in Enzymology volume 
183,
  pages 570-583, 1990.  Bootstrapping is used to analyze the statistical error
of
  the results.  Output files from CLUSTAL and  PILEUP,  as  well  as  some 
other
  formats,  can  be used for input, and analysis can be confined to certain
codon
  positions in coding sequences.  The program is written in FORTRAN and  runs 
on
  VMS  systems.   It  was  produced  by Dr. Graziano Pesole and Professor
Cecilia
  Saccone at the University of Bari, Italy, and is available (for free?) from
Dr.
  Cecilia  Lanave at CSMME-CNR, Dipartimento di Biochimica e Biologia
Molecolare,
  Universita` di Bari, via Orabona 4, 70126 Bari, Italy.   Her  phone  number 
is
  39-80-243305,  her  fax  number  is  39-80-243317,  and  her  e-mail address
is
  lanave at vaxba0.ba.it or mvx36 at ibacsata.it
  
       18. J. S.  Farris  and  Mary  Mickevich  earlier  released  a  package 
of
  phylogeny programs, PHYSYS, which, at about $5,000, was extremely expensive
(in
  my opinion, which is certainly a biased one).  I  am  not  sure  whether, 
from
  whom, or under what conditions it is still available.
  
       19.  Fujitsu Ltd. ("a $21 billion  global  leader  in  advanced 
computer,
  telecommunications,  and  electronic devices") sells for $28,000 US a Fujitsu
S
  family  workstation  complete  with  a   program,   SINCAIDEN,   which  
allows
  "experimental  researchers,  even  those  unfamiliar  with  such analyses,
[to]
  easily create phylogenetic trees in their own laboratories."  The program 
also
  allows  searches  of the major nucleic acid sequence and protein databases
(the
  ad I saw does not make it clear whether these databases are provided  with 
the
  workstation).   The  methods  available  are  UPGMA, neighbor-joining,
Farris's
  (Distance Wagner)  and  the  modified  Farris  distance  matrix  methods.  
The
  workstation  is  SPARC  compatible  and  runs SunOS.  The SYNCAIDEN program
was
  developed by the group at the National Institute of Genetics, Japan  under 
Dr.
  Takashi  Gojobori.   Fujitsu  Ltd. may be contacted at 21-8, Nishi-Shinbashi
3-
  chome, Minato-ku, Tokyo 105, Japan (phone 81-3-3437-5111 ext. 2831,  fax 
81-3-
  5472-4354),  or  in  the  U.S. at Fujitsu America Inc., 3055 Orchard Drive,
San
  Jose, California 95134-2017 (phone 1-408-432-1300  ext.  5168,  fax 
1-408-434-
  1045).
  
       20.  MUST, a package of sequence management programs, is distributed on 
a
  shareware  basis  by  Herve  Phillippe, Laboratoire de Biologie Cellulaire
(URA
  CNRS 1134 D), Batiment 444, Universite de Paris-Sud, 91405 Orsay cedex,
France.
  His  e-mail  address  is:  adoutte at frciti51  on Bitnet/EARN.  His phone and
fax
  numbers  are  respectively  33.1.69.41.64.81  and  33.1.69.41.21.30.   MUST 
is
  available  on  a  shareware  basis  ($100  registration  fee if you do not
send
  diskettes) and runs on PCDOS systems using PCDOS version 3  or  later.   It 
is
  intended  as complementary to existing phylogeny and alignment programs and
can
  produce output files in the formats of PHYLIP, PAUP, Hennig86, and CLUSTAL. 
It
  contains a variety of sequence input, editing, checking, and storage
functions,
  as well as a sequence editor and a phylogeny plotter.  It also  allows 
further
  analyses of the results from these phylogeny programs.
  
       21.  Steve Smith, formerly of the Harvard Genome Laboratory,  has 
written
  an  X-Windows interactive sequence editor, GDE (Genetic Data Environment)
which
  allows the user to edit sequences and align them by hand, and to select
subsets
  of  sites  and  sequences  and  call  a  variety of analysis proprams
including
  ClustalV and many of the PHYLIP 3.4 programs.  The GDE 2.0 system will  run 
on
  many  workstations  that  have  the  X  windowing system.  It also includes
the
  TreeTool tree-plotting program (see below).  GDE 2.0 is free and  is 
available
  for  anonymous  ftp  transfer  at  either  at  golgi.harvard.edu  in 
directory
  pub/GDE2.0 and also at ftp.bio.indiana.edu in directory molbio/unix/GDE.
  
       22.  Mike Maciukenas, at the Department of Microbiology of the 
University
  of  Illinois, has written a wonderful X-windows based interactive
tree-plotting
  program called TreeTool.  It takes as input a PHYLIP  tree  file,  with 
branch
  lengths  if  they  are provided, displays the tree in either rooted or
unrooted
  form on any X-windows screen, and allows the user to modify  the  form  of 
the
  tree and the placement of nodes and labels.  When the tree is in final form
the
  user can have it written to a Postscript file and/or printed to  a 
Postscript-
  compatible  printer.   TreeTool  is  free  as  a C program for X windows and
is
  available   for   anonymous   ftp   from   ftp.bio.indiana.edu   in  
directory
  molbio/unix/GDE.   It  is  also  included  in  the  GDE  2.0  sequence
analysis
  environment mentioned above.
  
  -----
  Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
   --> Internet:         joe at genetics.washington.edu     (IP No. 128.95.12.41)
       Bitnet/EARN:      felsenst at uwavm
  
  
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