Over the years various granting agencies have contributed to the support of the PHYLIP project (at first without knowing it). They are:

Years       Agency                       Grant or Contract Number

1992-1995   National Science Foundation  DEB-9207558
1992-1994   NIH NIGMS Shannon Award      2 R55 GM41716-04
1989-1992   NIH NIGMS                    1 R01-GM41716-01
1990-1992   National Science Foundation  BSR-8918333
1987-1990   National Science Foundation  BSR-8614807
1979-1987   U.S. Department of Energy    DE-AM06-76RLO2225 TA DE-AT06-76EV71005
I am particularly grateful to program administrators William Moore, Irene Eckstrand, Peter Arzberger, and Conrad Istock, who have gone beyond the call of duty to make sure that PHYLIP continued.

Booby prizes for funding are awarded to:

  1. The people at the U.S. Department of Energy who, in 1987, decided they were "not interested in phylogenies",
  2. The members of the Systematics Panel of NSF who twice (in 1989 and 1992) positively recommended that my applications NOT be funded. I am very grateful to program director William Moore for courageously overruling their decision the first time. The current (1992) Systematics Panel can claim no credit for PHYLIP whatsoever.
  3. The members of the 1992 Genetics Study Section of NIH who rated my proposal in the 53rd percentile (I don't know if that's 53rd from the top or the bottom, but does it matter?), thus denying it funding. I am, however, grateful to the NIGMS administrators who supported giving me a "Shannon award" partially funding my work for a period in spite of this rating.
The original Camin-Sokal parsimony program and the polymorphism parsimony program were written by me in 1977 and 1978. They were Pascal versions of earlier FORTRAN programs I wrote in 1966 and 1967 using the same algorithm to infer phylogenies under the Camin-Sokal and polymorphism parsimony criteria. Harvey Motulsky worked for me as a programmer in 1971 and wrote FORTRAN programs to carry out the Camin-Sokal, Dollo, and polymorphism methods. But most of the work on PHYLIP other than my own was by Jerry Shurman and Mark Moehring. Jerry Shurman worked for me in the summers of 1979 and 1980, and Mark Moehring worked for me in the summers of 1980 and 1981. Both wrote original versions of many of the other programs, based on the original versions of my Camin-Sokal parsimony program and POLYM. These formed the basis of Version 1 of the Package, first distributed in October, 1980.

Version 2, released in the spring of 1982, involved a fairly complete rewrite by me of many of those programs. Jerry and Mark are not to be held responsible for problems arising from use of these programs. Hisashi Horino has for version 3.3 reworked some parts of the programs CLIQUE and CONSENSE to make their output more comprehensible, and has added some code to the tree- drawing programs DRAWGRAM and DRAWTREE as well.

My part-time programmers Akiko Fuseki, Sean Lamont and Andrew Keeffe gave me substantial help with the current release, and their excellent work is greatly appreciated. Akiko in particular did much of the hard work of adding new features and changing old ones in the 3.4 and 3.5 releases, and Andrew prepared the Macintosh version, wrote RETREE, and added the ray-tracing and PICT code to the DRAW programs. Sean was central to the conversion to C, and tested it extensively. My postdoctoral fellow Mary Kuhner and her associate Jon Yamato created NEIGHBOR, the neighbor-joining and UPGMA program, for the current release, for which I am also grateful (Naruya Saitou kindly encouraged us to use some of the code from his own implementation of this method).

I am very grateful to many users for algorithmic suggestions, complaints about features (or lack of features), and information about the behavior of their operating systems and compilers. Among these are:

   Jim Archie               Timothy Goldsmith        Dan Nickrent
   Mary Barkworth           Rees Griffiths           Trang Nguyen
   Yves Bertheau            George Gutman            Cary O'Donnell
   Vincent Bauchau          Linda Hardison           Steve O'Kane
   Bernard Baum             Gene Hart                Gary Olsen
   Mary Berbee              Masami Hasegawa          John Olsen
   Biff Bermingham          Bill Hatheway            Steve O'Neill
   Yves Bertheau            David Hillis             Greg Orloff
   Pierre Boursot           Richard Holliday         Pekka Pamilo
   Tom Bruns                Eddie Holmes             David Penny
   Tsan Iang Chuang         Kent Holsinger           Norman Platnick
   Stephen Clark            Dan Hough                Mark Ragan
   Bruce Cochrane           Richard Jensen           Neil Rawlings
   Joel Cracraft            Bo Johansson             Tom Ritch
   Ross Crozier             Quentin Kay              Alistair Robertson
   Mark Dalton              Steve Kelem              Joseph R. Rohrer
   Dan Davison              Kim Cheol-Min            Naruya Saitou
   Ron DeBry                Joseph H. Kirkbride      Kay Schneitz
   Allen Delaney            John Kirsch              Paul Sharp
   Terry Delaney            Andrew Knight            Arend Sidow
   John Devereux            Dennis Knudson           Hans Siegismund
   Tod Distotell            Mary Kuhner              Chuck Smart
   John Doebley             Jan Kwiatowski           Douglas Smith
   Ken Dodds                John LaDuke              Dave Spencer
   Jim Doyle                Lionel Landry            Lisa Steiner
   Guy Drouin               Franz Lang               Per Sundberg
   Shan Duncan              Niels Larsen             Susan Swensen
   Tom Duncan               Jerry Learn              David Swofford
   Robert Eaglen            Rev. Arthur Lee          John Sved
   Scott Edwards            Pierre Legendre          Naoko Takezaki
   Willem Ellis             Jack A.M. Leunissen      Eric Taylor
   Ted Emigh                Andrew Lloyd             Jeff Thorne
   John Endler              Wolfgang Ludwig          Clive Trotman
   Laurent Excoffier        David Maddison           John Turnbull
   James Farmer             Wayne Maddison           Hans Ullitz-Moeller
   David Featherston        George McKay             Michael Vodkin
   Kent Fiala               Brian McMahon            Carl Wadsworth
   Tim Flannery             Christopher Meacham      Ryk Ward
   Vera Ford                Brook Milligan           Daniel Weeks
   Kurt Fristrup            Sanzo Miyazawa           Loni West
   Douglas Futuyma          Janice Moore             George D.F. Wilson
   Michael Garrick          Susumu Nakayama          Thomas K. Wilson
   Don Gilbert              Jean-Marc Neuhaus        M. Zandee
   John Gillespie           Haolin Ni                Eric Zurcher
   Nick Goldman
My apologies to anyone who has accidentally been left out of this list. Keep making suggestions and you will get on eventually.

A growing contribution to this package has been made by others writing programs or parts of programs. Chris Meacham contributed the important program FACTOR, long demanded by users, and the even more important ones PLOTREE and PLOTGRAM. Important parts of the code in DRAWGRAM and DRAWTREE were taken over from those two programs. He is thus mostly to blame for all problems with these programs. Kent Fiala wrote PROCEDURE reroot to do outgroup-rooting, which was an essential part of many programs in earlier versions. Someone at the Western Australia Institute of Technology suggested the name PHYLIP (by writing it on a magnetic tape as the tape label), but they all seem to deny having done so (and I've lost the relevant letter).

Arend Sidow contributed makeinf.c to the Unsupported Division of this release, and Masami Hasegawa and Jun Adachi contributed ProtML.pas. Their generosity is much appreciated.

The distribution of the package also owes much to Buz Wilson and Willem Ellis, who have put a lot of effort into the past distribution of the PCDOS and Macintosh versions respectively. Christopher Meacham and Tom Duncan for three versions distributed a printed version of these documentation files (they are no longer able to do so), and I am very grateful to them for those efforts. William H.E. Day and F. James Rohlf have been very helpful in setting up the listserver news bulletin service.

I also wish to thank the people who have made computer resources available to me, mostly in the loan of use of microcomputers. These include Jeremy Field, Clem Furlong, Rick Garber, Dan Jacobson, Rochelle Kochin, Monty Slatkin, Jim Archie, Jim Thomas, and George Gilchrist.

I should also acknowledge the computers used to develop this package: These include a CDC 6400, two DECSystem 1090s, my trusty old SOL-20, my old Osborne-1, a VAX 11/780, a VAX 8600, my old MicroVAX I, my old DECstation 3100, my old Toshiba 1100+, and my present mainstays, a DECstation 5000/200, a DECstation 5000/125, a Compudyne 486DX/33, a Trinity Genesis 386SX, a Zenith Z386 and a Mac Classic. (One of the reasons we have been successful in achieving compatibility between different computer systems is that I have had to run them myself under so many different operating systems and compilers).

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Maintained 15 Jul 1996 -- by Martin Hilbers(