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-AT06-76EV71005I 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:
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 GoldmanMy 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).