HOW YOU CAN HELP ME

Simply let me know of any problems you have had adapting the programs to your computer. I can often make "transparent" changes that, by making the code avoid the wilder, woolier, and less standard parts of C, not only help others who have your machine but even improve the chance of the programs functioning on new machines. I would like fairly detailed information on what gave trouble, on what operating system, compiler and machine, and what had to be done to make it work. I will be pleased to help do some over-the-telephone trouble-shooting, particularly if I don't pay for the call. Electronic mail is a particularly convenient way for me to be asked about problems, as you can include your input and output files so I can see what is going on. I'd really like these programs to be able to run with only routine changes on ABSOLUTELY EVERYTHING, down to and possibly including the Amana Touchmatic Radarange Microwave Oven (which is an Intel 8080 system -- early versions of this package did run successfully on Intel 8080 systems).

I would also like to know timings of programs from the package, when run on the three test input files provided above, for various computer and compiler combinations, so that I can provide this information in the section on speeds of this document.

For the phylogeny plotting programs DRAWGRAM and DRAWTREE, Chris Meacham and I are particularly interested in knowing what has to be done to adapt it for other common plotters, laser printers, and dot matrix printers.

You can also be helpful to PHYLIP users in your part of the world by giving them the latest version of PHYLIP and helping them with any problems they may have in getting PHYLIP working on their data.

Your help is appreciated. I am always happy to hear suggestions for features and programs that ought to be incorporated in the package, but please do not be upset if I turn out to have already considered the particular possibility you suggest and decided against it.

I would also like to know of any applications of PHYLIP that get published: I would appreciate receiving a reprint of any paper reporting work that used PHYLIP.

LISTSERVER BULLETINS

Through the kind assistance of F. James Rohlf and William H.E. Day, starting with version 3.2 an electronic version of the PHYLIP Newsletter has been available. Using software called a "listserver", on a mainframe at State University of New York, I can store files which you can retrieve simply by sending the listserver a series of commands.

Initially there will be four files:

GENERAL: This file describes the PHYLIP package and how to order it. It will be kept up to date, with descriptions of new ways to get PHYLIP and will reflect the latest version.
NOTICES: This contains news about PHYLIP. It will describe recent changes in distribution methods, expected release dates and contents of new versions, as well as occasional news about other phylogeny computer programs. Items will be stored in reverse order so you can stop reading it when you see something you have already read.
NEWBUGS: A list of recently found bugs in PHYLIP. This will change from time to time, the old bugs being added to BUGLIST.
BUGLIST: This contains a cumulative list of all bugs, and (if possible) their fixes. Again, these will be stored in reverse order. The most recent bugs will be described in NEWBUGS, the older ones in BUGLIST.

To get copies of these three files you have to send commands to LISTSERV@CCVM.SUNYSB.EDU (on Internet), or LISTSERV@SBCCVM on BITNET (or EARN). Directions for sending commands are given below.

The first time you use the listserver, if your name is (say) Ralph Foobar, send the command:

SUB CLASS-L "Ralph Foobar"

This enters your subscription to CLASS-L. Then you can request the four individual files mentioned above by sending three commands:

GET PHYLIP GENERAL CLASS-L

GET PHYLIP NOTICES CLASS-L

GET PHYLIP NEWBUGS CLASS-L

GET PHYLIP BUGLIST CLASS-L

or a single command with the same effect:

GET PHYLIP PACKAGE CLASS-L

If you want to be placed on a list to receive the new copies of any of these three files whenever they are updated (Automatic File Update), you first must define a password for yourself. To use the password "KLUTZ", send the command:

PW ADD KLUTZ

Then use the password with the AFD commands:

AFD ADD PHYLIP GENERAL PW=KLUTZ
AFD ADD PHYLIP NOTICES PW=KLUTZ
AFD ADD PHYLIP NEWBUGS PW=KLUTZ

I am assuming that you don't want a complete copy of the BUGLIST each time it is updated, as you are getting all the NEWBUGS entries and saw the BUGLIST once (it is big and cumbersome).

If you do not want to receive the files automatically but want instead to receive automatically notices that the files have been updated (File Update Information), send the command:

FUI ADD PHYLIP PACKAGE PW=KLUTZ

There are two ways to deliver commands to LISTSERV@CCVM.SUNYSB.EDU: by electronic mail (which ought to work from any electronic mail network) or by interactive messages (which will work if you're at a BITNET node). To send commands by electronic mail, simply send your commands as the text body of an electronic mail message, one command per line. For example, you could send to LISTSERV@CCVM.SUNYSB.EDU the following commands in a single electronic mail message with six lines of text:

SUB CLASS-L "Ralph Foobar"
GET PHYLIP PACKAGE CLASS-L
PW ADD KLUTZ
AFD ADD PHYLIP GENERAL PW=KLUTZ
AFD ADD PHYLIP NOTICES PW=KLUTZ
AFD ADD PHYLIP NEWBUGS PW=KLUTZ

If you wish to use interactive messages, check with your local "guru" about how to send one-line interactive messages. If you have a TELL command, for example, then you would send a sequence of four messages such as:

TELL LISTSERV AT SBCCVM SUB CLASS-L "Ralph Foobar"

If you encounter problems and can't get answers locally, Stuart Campbell (scampbel@ccvm.sunysb.edu), Jim Rohlf (rohlf@biovm.sunysb.edu) or Bill Day (whday@mun on BITNET) might be able to help you.

There are many other services of CLASS-L including distribution of some peoples' programs (not mine at the moment) and a "bulletin board" service. The file PHYLIP GENERAL will describe some of the commands you need for those services, and where you can get additional information.

This electronic news bulletin service has taken over from the mail distribution of printed newsletters by me; there will be no more printed newsletters as these are too expensive and time-consuming to print and mail.

IN CASE OF TROUBLE

READ THE DOCUMENTATION FILES CAREFULLY ("RTFM"). If that doesn't solve the problem, get in touch with me. I am on electronic mail at the addresses given below. If you do ask about a problem, please specify the program name, version of the package, computer and compiler, and be prepared to send me your data file so I can test the problem. Also it helps to have the relevant input and output and documentation file nearby so that we can refer to it. I can also be reached by calling me in my office: (206)-543-0150, or at home: (206)- 526-9057 (how's THAT for user support!). If I cannot be reached at either place, a message can be left at the office of the Department of Genetics, (206)-543-1657 but I prefer strongly that I not call you, as in any phone consultation the least you can do is pay the phone bill.

Particularly if you are in a part of the world distant from me, you may also want to try to get in touch with other users of PHYLIP nearby. I provide a list of nearby users when I ship you the package and can on request try to supply more recent information.

Electronic mail addresses (I prefer that you use the Internet address
if possible):
Internet (NSFNET):           joe@genetics.washington.edu
                             joe@evolution.genetics.washington.edu
                             joe@128.95.12.41

Bitnet (EARN, NETNORTH):     joe%genetics@UWAVM
                             FELSENST@UWAVM
                             FELSENST@UWAVM.U.WASHINGTON.EDU

UUCP:                        ... uw-beaver!evolution.genetics!joe




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Maintained 15 Jul 1996 -- by Martin Hilbers(e-mail:M.P.Hilbers@dl.ac.uk)