Other phylogeny programs available elsewhere

Joe Felsenstein joe at GENETICS.WASHINGTON.EDU
Wed Jun 6 01:52:26 EST 1990

My apologies for posting a 153-line message.  The following is material
from the PHYLIP version 3.3 manual about programs distributed by others.
Since I have just used the net to advertise my own programs, the programs
by others should be mentioned too.

     Here are some of the other phylogeny packages that I know about:

     1.  David Swofford (Illinois Natural  History  Survey,  Natural  Resources
Building,   607   East  Peabody  Drive,  Champaign,  Illinois   61820,  U.S.A.)
distributes PAUP (Phylogenetic Analysis Using Parsimony).

     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 (May, 1990) he was about to release version 3 (PAUP/Mac) for
the  Macintosh,  and  later  in  the  year hopes to release version 3 for PCDOS
systems and ultimately for mainframes.  Its cost is $50.  Orders  received  for
the Mac version before its release will be filled but the printed documentation
will arrive later, after the formal release.

     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 $35.00.  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.  As of  this  writing  it  was  distributed  by  Wayne  Maddison,
Department   of   Integrative  Biology,  University  of  California,  Berkeley,
California 94720. U.S.A.   David  Maddison  and  he  have  produced  a  program
enabling  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.  Version  2.1  was
released  in  March  1987.  Version 3, with a spread-sheet data editor, support
for polytomies, charting facilities, PHYLIP, PAUP, and HENNIG86  compatibility,
and many other new features, is coming soon.  The program is originally written
in Lightspeed Pascal but is provided in pre-compiled form, and is available for
distribution cost ($6 in North America, $8 overseas, or three or four Macintosh
diskettes in barter).  It requires a 512K Macintosh, Macintosh Plus, or larger.
In  the near future the distribution of version 3 will be on a commercial basis
by Sinauer Associates of Sunderland, Massachusetts, although versions 1  and  2
will  continue  to  be  freely  distributable.   Version 2 is also available by
electronic mail from the EMBL and Houston net  servers  which  distribute  free
software for molecular data analysis, in their Mac software.

     4.  J. S. Farris (41 Admiral Street,  Port  Jefferson  Station,  New  York
11776,  U.S.A.)  has  produced  Hennig86,  a  fast  parsimony program including
branch- and-bound search for  most  parsimonious  trees  and  interactuve  tree
rearrangement.   Although complete benchmarks have not been published it may be
a bit 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.

     5. Jotun Hein, currently  at  the  Universite  de  Montreal  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.   The  program is large, and is available in C
source from either the EMBL or the Houston net  servers,  from  which  you  can
fetch  PC, Mac, or VAX programs free for molecular data.  On EARN or BITNET you
can send an electronic mail message to NETSERV at EMBL  with  a  "Subject: "  line
that  reads   HELP SOFTWARE.  On BITNET or Internet you can send to the Houston
server which is: genbank-server at uhnix2.uh.edu a message that has a  "Subject: "
line:  SEND UNIX HELP or SEND VMS HELP to receive a file telling you how to get
further sofware from them, including TreeAlign.  TreeAlign uses so much  memory
that it cannot be run on PC's (DOS or Mac systems) but is really designed for a
workstation or  mainframe.   You  can  also  get  TreeAlign  over  Internet  by
anonymous   ftp   from  lavaca.uh.edu  from  the  appropriate  subdirectory  of

     6.  David Penny (Department of  Botany  and  Zoology,  Massey  University,
Palmerston  North,  New  Zealand)  has  offered  (I  believe  for  free) a fast
parsimony program, TurboTree.  Contact him for details.

     7. Andrey A. Zharkikh, Yu.  V.  Rzhetsky,  and  their  co-workers  in  the
Institute  of Cytology and Genetics, Siberian Branch of the Academy of Sciences
of the USSR, Novosibirsk 630090,  USSR  are  offering  VOSTORG,  a  package  of
programs for alignment and analyzing phylogenies for molecular sequences on IBM
PC-compatibles that include some rather fancy graphics.   I  do  not  know  the
exact  conditions  of  distribution:  Zharkikh and Rzhetsky ask that interested
parties contact them at that address.

     8. Joyce Miller of  the  Department  of  Plant  Pathology,  University  of
Wisconsin, 1630 Linden Drive, Madison, Wisconsin  53706 is offering RESTSITE, a
program for PC-compatibles to construct phylogenies from  restriction  site  or
restriction fragment data.  It is distributed for free (send her two 360K PCDOS
floppy diskettes) and includes  programs  to  compute  genetic  distances  from
restriction  site  or fragment data and two PCDOS computer programs to do UPGMA
and neighbor-joining methods for constructing  phylogenies  from  the  distance
matrices.  Some source code is also included.

     9. J. S. Farris 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).

     10.  Kent Fiala's program CLINCH  is  available  for  doing  compatibility
analysis  of  characters.  Fiala's program finds largest cliques of characters.
It has more options and can handle more kinds of data  than  the  compatibility
program  in PHYLIP.  It is available in both mainframe and IBM PC versions (PC-
CLINCH), for free.  It is written in FORTRAN, and for the IBM PC  the  compiled
source code is also distributed.  For information, write Kent Fiala (Department
of Ecology and Evolution, SUNY, Stony Brook, New York 11794, U.S.A.),

     11.   Walter  Fitch  (Department  of  Ecology  and  Evolutionary  Biology,
University  of California, Irvine, California  92717, U.S.A.) has available, as
far as I know for free (or for media and  mailing  cost),  a  large  number  of
FORTRAN  programs  for  not  only  estimating  trees  but  doing  various other
manipulations of data that might be needed in studies  of  molecular  evolution
(for  example,  looking  for  homologies among sequences).  These programs were
originally written for the Univac system at Wisconsin  He  has  gradually  been
rewriting  these  to  work  on microcomputers, and as he does so, Fitch will be
releasing them; some are available already.

     12. Philip Taylor (MRC  Institute  of  Virology,  University  of  Glasgow,
Glasgow  G11  5JR,  U.K.)  offers  a  FORTRAN-66 program, DENDRON, for distance
matrix analyses, which he says obtai

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