PHYLIP was first released in 1980. Here are some people whose participation has been important:

Early programming:

• Jerry Shurman
• Mark Moehring

Distribution of different versions: these people pioneered the various forms of distribution, but all versions are now distributed by us.

• Thomas Wilson (CP/M executables)
• Buz Wilson ([no relation to Tom], DOS executables)
• Willem Ellis (Mac executables)
• Alan Rogers (ftp site)

Important contribution of program code

• Christopher Meacham (UC Berkeley) for FACTOR, predecessors of DRAWGRAM and DRAWTREE.
• Mary Kuhner, Jon Yamato, and Naruya Saitou for contributions of code for the Neighbor-Joining program NEIGHBOR.

Further programming:

• Hisashi Horino (draw program drivers)
• Sean Lamont (draw program drivers, C conversion, fixing workstations and network)
• Akiko Fuseki (much algorithmic programming and C conversion)
• Dan Fineman (consensus tree program, draw program drivers)
• Patrick Colacurcio (tree reading code)
• Daniel Yek, (algorithmic programming)
• Doug Buxton (completion of 3.6b release)
• Rev. Dr. Lucas Mix (Proml and Promlk)
• Andrew Keeffe (especially interactive tree manipulation programs)
• Mike Palczewski (3.6 release, customization for compilers, GUI, major revision of code base)
• Marissa LaMadrid (testing for bugs)
• Ian Robertson (especially wizard computer configuration)
• Eric Rynes (work on a future codon-model program)

Current programmers are:

(When they're not working on LAMARC)

• Elizabeth Walkup
• Bob Giansiracusa
• Jim McGill

Grant support

Years	granting agency	grant number
2011-2013	National Science Foundation	DEB-1019583
2011-2012	National Science Foundation	Cooperative agreement DBI-0939454
2005-2009	NIH NIGMS	R01 GM071639
1999-2003	National Science Foundation	DEB-9815650
1996-1999	National Science Foundation	BIR-9527687
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

No thanks to

• US Department of Energy, 1987 ("not interested in phylogenies")
• The reviewers at NSF Systematic Biology panel in 1990 ("rating: Do Not Fund") who were then courageously overruled by program director William Moore.
• NSF Systematic Biology Panel, 1992 ("rating: Do Not Fund")
• 1992 Genetics Study Section of NIH ("rating: 53rd percentile")
• The reviewers at NSF Population Biology in early 2003 who gave my proposal too anemic a rating: ("The work has the potential to define the field for many years to come .... All agreed that the proposal is somewhat vague. There was also some concern that the proposed work is too ambitious.")
• The reviewers at the Genetics Study Section of the NIH in early 2004 who said such nice things about my proposal ("One is likely to look back in 20 years and marvel that these questions were not actively pursued by more theoreticians" and "The first inclination is to give this PI all the money he wants!"), but then proceeded to give my proposal a 30.2 percentile rating. Next time you can tone down the praise as long as you improve the ratings, OK? [Perhaps they listened to this. The next time through, a different panel (the new Genetic Diversity study section), said nice but more restrained things while giving a very high rating to the proposal]
• The NIH program on Continued Development and Maintenance of Software, 2008 who rated my proposal for continued development of PHYLIP at a percentile of 50.6 ("While PHYLIP is much acclaimed for its impact over the years, the application is not considered significant given the state of the art today and what is being proposed. The application is deficient in a rigorous comparative analysis of other tools and the Panel comments on the lack of software engineering expertise. Overall, the application is considered average in its present form despite the excellence of the investigator who is highly respected.") There's one more NIH program to avoid -- they don't seem to fund continued development and maintenance of software. I wonder -- when we look back a few years from now, will we find that the computer programs which they did support ended up getting more use than PHYLIP?
• The NSF Assembling the Tree Of Life (AToL) Spring 2008 Advisory Panel who decided that a grant proposal by me and Fred Bookstein to develop Brownian Motion models for morphological characters, and methods of applying them to fossil data and to use morphometrics, was Meritorious but was Not Fundable. ("All of the panelists and reviewers were enthusiastic about the goals, and expressed great respect for the previous work of the investigators. However, there were significant weaknesses in the proposal would have been enhanced by some proof-of-concept or other preliminary results or examples, more specific information regarding approaches to statistical issues, and a better overall integration of the two main components of the proposal. An additional team member providing paleobiological/stratigraphic expertise would enhance the project's viability. Finally, the panel believes that education and outreach should be addressed more explicitly.") I guess the thousands of distributions of PHYLIP, the many lectures and articles I have written on phylogenies over the years, weren't "outreach".
• The NSF Assembling the Tree of Life (AToL) Spring 2009 Advisory Panel, who decided that the revised grant proposal by me and Fred Bookstein was once again Meritorious but Not Fundable. Here is part of the panel summary statement:

  CRITERION I Intellectual Merit Intellectual Strengths: The panel was very enthusiastic about the need for new programs that would advance model-based approaches to evaluating morphology for phylogenetic analysis. Should these methods be developed, they could also be applied to giving a direct role to morphology in tree building and to providing better tools for molecular dating. Intellectual Weaknesses: No taxonomic test cases were identified for the new method. Members of the panel expressed concerns that morphometrics does not currently play a significant role in large scale morphological systematics, thus it was not clear why expanded funding for morphometrics was a priority. CRITERION II Broader Impact Broader Impact Strengths: The panel recognizes the important contributions that the PIs have made both in theory and in tool development, and that this constitutes a form of broader impact that may continue in the future. Broader Impact Weaknesses: No specific plans were given to train younger investigators or to provide significant outreach to the public or non-university educators. SYNTHESIS AND RECOMMENDATION The PIs propose to develop software that integrates molecular phylogenetics and morphometrics. They predict that development of this software will enhance the role of morphology in systematics because it will allow morphology to be approached with model-based algorithms. The panel was unanimously enthusiastic about the need to expand model-based approaches to the investigation of morphology; however, there was not agreement that the proposed approach using morphometrics was likely to contribute to higher level phylogenetic questions.

  That's the last time I try to go to NSF AToL for money -- they clearly do not fund development of methods (or understand how it is done).

• In 2010 Fred and I applied once more to the NSF Systematics and Biodiversity Program. Once again the reviewers trashed the grant proposal. They rated it Not Competitive. (I will publish the summary here soon). This time the program chair, Maureen Kearney, courageously overruled them and we got the money.
• A preproposal by us for continued work in 2014 failed to get a strong enough rating to enable us to make another application. Through most of 2014 we had a dribble of no-cost extension money, left over from the grant that was awarded in 2010, being spent for part of our salaries. This ended at the end of October, 2014. Currently I have no grant funding.

A few thoughts about the above list:

• Does all this “outreach” stuff mean I have to devote time to giving workshops to mystified culinary arts students? These grants are for development of advanced methods, and briefing “the public or non-university educators” about those methods would seem to be a waste of time -- though I do spend some effort on fighting creationists and Intelligent Design advocates, but I don't bring up these methods in doing so.
• Does all this “preliminary examples” stuff mean that we have to have methods completed before applying for money to develop them?
• Do all the calls for a larger training component or bringing a paleontologist on board mean that they will look favorably on a 25-50% expansion of the proposal budget? Who's kidding who?

Hero Medals for standing up for us at considerable personal risk to

• William Moore, NSF and Wayne State University. In 1990 as head of the NSF program funding systematics, he actually overruled his panel, which had recommended that a grant of mine positively not be funded, and awarded the grant.
• Maureen Kearney, program head of NSF Systematics and Biodoversity. On the 20th anniversary of Bill Moore's brave action, she did the same. My thanks to her for sticking out her neck and acting on her convictions.

Thanks for helping us find funds to

• Irene Eckstrand, NIH Genetics Study Section
• Peter Arzberger, (then of) NSF Computational Biology

Much helpful advice from

• David Swofford
• Gary Olsen
• Wayne Maddison
• David Maddison
  (if PHYLIP is better in any ways than their programs, it's because they were generous in sharing their techniques).

Inspiration to keep going came from

• Cladistics magazine, for endless negative reviews and disparaging comments. If they liked it I'd worry.

  (I do note that the Hennig Society page for Cladistics includes a link for most-cited papers. The list is only of recent papers. My 1989 note in Cladistics describing PHYLIP, on page 164 of volume 5, is in fact the most cited paper ever in that journal, responsible for at least 15% of all citations to the journal, and making me the second-most-cited-ever author in that journal! You'd think they'd like me.)

And many thanks to about 300 users for complaints, suggestions, bug fixes, and much more.

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