Puzzle
Puzzle is implemented in the PUZZLE subdirectory of the S: drive and will also be placed on the Mac if requested. The authors own manual is there as manual.htm but also placed as support here as puzzle.htm. Please note that the authors request that it be unaltered and I have respected that request (except to update an in press citation).

***

Here is how to get some of them:

The tree of life is a very general resource.

COMPUTER RESOURCES-

The most extensive package is Phylip by Joe Felsenstein. It is freely shared with provisos in the docs. Here is how to get it:

GETTING PHYLIP 3.5 BY ftp

Anyone with an Internet connection can now get PHYLIP 3.5 (my package of computer programs for inferring phylogenies) using "anonymous ftp". PHYLIP sources and executables exist for ftp distribution in four forms. One is as "compressed tar archives", a system of storing many files as one file and then compressing the size of the file that is used in Unix systems. Another is as self-extracting PCDOS archives. A third is as self-extracting MacBinary II archives created by CompactPro, an archiving program used on Macintoshes and PowerMacs. The fourth is the BinHex format for the self- extracting Macintosh archives. The names of the available archives are
Contents Form Name
-------- ---- ----
C Sources and docs Compressed tar phylip.tar.Z
Pascal Sources and docs Compressed tar phylipp.tar.Z
C Sources and docs PCDOS Self-extracting phylip.exe
Pascal Sources and docs PCDOS Self-extracting phylipp.exe
PCDOS executables PCDOS Self-extracting phylippx.exe/phylippy.exe
386 PCDOS executables PCDOS Self-extracting phylip3x.exe/phylip3y.exe
386 Windows executables PCDOS Self-extracting phylipwx.exe/phylipwy.exe
/phylipwz.exe
C Sources and docs Self-extracting CompactPro phylip.sea.bin Pascal Sources and docs Self-extracting CompactPro phylipp.sea.bin Macintosh executables Self-extracting CompactPro phylipmx.sea.bin PowerMac executables Self-extracting Compactpro phylippmac.sea.bin C Sources and docs Self-extracting BinHex phylip.sea.hqx Macintosh executables Self-extracting BinHex phylipmx.sea.bin You will only want to get PHYLIP in one of the four forms of archive, and generally you will need one of the two kinds of the Sources and documentation files, as the executables archives have essentially no documentation in them. To extract the Compressed tar archives you need to use the utilities "uncompress" and "tar" which are standard on almost all Unix systems. Other mainframe or workstation operating systems may have utilities to do the uncompression and the extraction of these archives. We do not any longer distribute separate executables for Sun, SGI, and DECstation systems, as the C source code of the package compiles easily on those systems using the "make" utility. To extract the self-extracting PCDOS archives, you can simply put them in a (big enough) directory on a PCDOS machine, and execute the archive as if it were a program! Each contains its own extraction program and will extract the separate files from the archive on its own. The self-extracting CompactPro archives were transferred to my workstation using the MacBinary protocol (hence the ".bin" suffix) and with the "binary" mode of ftp set. They should be downloaded to a Macintosh using the "binary" setting (if relevant) and the MacBinary protocol. They can then be extracted using the CompactPro archiver, or ... you can simply put them in a (big enough) disk area on a Macintosh and double click on them. They will then present an opportunity to choose the directory the files go into, and on clicking on the "Extract" button will unstuff themselves into a number of subdirectories and many files. The self-extracting BinHex archives were also made by CompactPro, and then translated into BinHex format. If you decide to use these you must do a binary ftp transfer and then use a program such as Unstiffit Lite to convert the files to self-extracting executables. These then extract when you double- click on them, into a directory that you are asked to choose. We will not describe this option further in the instructions below. How to Transfer the Files by ftp Here is how to use ftp to transfer the archives and how to extract the files from them: 1) Make sure you have enough room for PHYLIP on your system. Most of the archives are compressed by a factor of 2-3, so that you will need enough space on your system to hold each archive (at least temporarily) plus the the files it extracts into. Thus if an archive is 1090k in size you may need 1090k+3270k of disk space to extract it, 3270k being needed permanently. Once you have connected to my machine by ftp, you will be able to see the archive file sizes by issuing a DIR command and can calculate whether you have enough space for the archives you want. 2) Use your local system's version of FTP to connect to my system, which is evolution.genetics.washington.edu. If your system says it has never heard of this address, try the number 128.95.12.41 instead. 3) In response to the "Name" or "Login" prompt, type "anonymous". In response to the "password:" prompt, type your full e-mail address. If you are using ftp from a VAX VMS system or from some Telnet programs you may have to type "user anonymous" to get to log in. It is important that the password you type be a proper e-mail address, preferably your full Internet address. 4) Once logged in, move into the directory "pub" by typing "cd pub". (On some systems the command may instead be "cwd pub".) 5) Move into the subdirectory "phylip" by typing "cd phylip". (On some systems the command may instead be "cwd phylip".) 6) Give the appropriate command to tell ftp that the data will be binary (on my system you type "binary"). If you are moving the files to a Macintosh, make sure that the step that transfers it to the Macintosh uses the "MacBinary" protocol. Some ftp programs such as "Fetch" usually do this automatically but many others require that you choose this option. 7) Look at the above list of archive names and types and decide what you want to get. If you are to get executables, make sure you also will get the source code and documentation archive. 8) To get the compressed tar archive version of the package, tell ftp to get the file phylip.tar.Z (on my system you type "get phylip.tar.Z"). To get the 386 PCDOS executables you will want to get three archives: the source code and documentation archive and two executables archives. Thus you might for example issue the commands: get phylip.exe get phylip3x.exe get phylip3y.exe Similarly for the generic PCDOS version, the 386 Windows version, or the Macintosh executables, you would issue commands to get the source code and documentation archive plus several executables archives. If you are transferring by ftp direct to a Macintosh the Macintosh or PowerMac self-extracting archives, it may be important at this point to ensure that the transfer used the MacBinary protocol. 9) Get out of ftp. (On my system you type "quit") 10a) If you are (say) going to move the self-extracting PCDOS archives to a PCDOS system by a file transfer program such as Kermit, that can now be done, keeping in mind that the archives are binary (not text) files and need to be transferred using the same methods as you would use for an executable program. Similarly, if you are instead using Internet to transfer the archives from one machine to another, use the "binary" mode for the transfer. 10b) (Macintosh CompactPro archives only). You can use a file transfer program to move the CompactPro archives to a Macintosh, but make sure that you enable the "MacBinary" mode which transfers binary files with all their attributes intact. If you use ftp to transfer the CompactPro archives to your Mac, make sure you also have the "image" (or "binary") mode set (as well as the MacBinary, mode so that the files transfer properly. If you use Versaterm to do the transfer to your Mac, make sure that you select "binary" in BOTH the "file" and "kermit commands" menus. To extract the archives simply place them in a disk area that has enough space and then double-click on the file. It will present a dialog box asking where the files should be put. Work your way through the directories, clicking appropriately, until you reach the one where you want them to go. Then click on "Extract". It should self-extract and form a number of folders. 11a) (PCDOS self-extracting archives only): Put each of the two archives in its own directory on a PCDOS system, and simply execute it as a program (i.e., for the file phylip.exe just type PHYLIP, for the archives like phylip3x.exe, and phylip3y.exe that have multiple parts, type the name of each part, PHYLIP3X and PHYLIP3Y). The archive will self extract and a series of files will appear in the directory. At this point you have succeeded. If all files were written you can now delete the archive to save space. 11b) (Tar archives only): If you are on a Unix system you will probably have a utility called "uncompress". Create and new directory and move the archive (say phylip.tar.Z) into it. You can simply issue the command: "uncompress phylip.tar.Z". When the command terminates you will find a file called "phylip.tar". The original compressed tar archive(s) will be gone. Unix systems also have a utility called "tar" that can unpack archives like phylip.tar. The command is most likely: "tar -xvf phylip.tar" (or analogously for other archive names). It will cause the files to be unpacked and placed in the current directory. If you do not have uncompress you will have to use pdtar or zcat instead. If you have pdtar (Public Domain TAR), you can do this by typing "pdtar zxvf phylip.tar.Z" on your system. If you have zcat, type "zcat phylip.tar.Z | tar xvf -". If this doesn't work, consult your local "guru", who may be able to tell you how to uncompress and unpack. 13) REGISTER YOUR COPY. Send electronic mail to me telling me that you have PHYLIP 3.5, which language (C or Pascal) you got the source code in, and which version of the executables you got, that you got these by anonymous ftp. and also tell me: Your name and address (no more than 5 lines total) Your telephone number and electronic mail address (together on 1 line) Name of your computer, operating system, and C or Pascal compiler (all of these together on 1 line) These should start in column 1 without indentation and fit into the required number of lines to make it easier for me to record them in my user database. For example, here is what this material would look like for me:
------------------------------- cut here -------------------------------
Joe Felsenstein Department of Genetics
SK-50 University of Washington
Seattle, Washington 98195 U.S.A.
+1-(206) 543-0150 (work), -0754 (fax),
joe@genetics.washington.edu
DECstation 5000/200 and 5000/125 with Ultrix 4.2 and DEC Ultrix RISC C compiler
------------------------------- cut here -------------------------------If you can do it in that format you will save me a lot of typing and editing. My email addresses are: Internet: joe@genetics.washington.edu joe@evolution.genetics.washington.edu joe@128.95.12.41 and my phone numbers are: Work: (206)-543-0150 Home: (206)-526-9057

The tree of life is a very general resource.

COMPUTER RESOURCES-

The most extensive package is Phylip by Joe Felsenstein. It is freely shared with provisos in the docs. Here is how to get it:

GETTING PHYLIP 3.5 BY ftp

Anyone with an Internet connection can now get PHYLIP 3.5 (my package of computer programs for inferring phylogenies) using "anonymous ftp". PHYLIP sources and executables exist for ftp distribution in four forms. One is as "compressed tar archives", a system of storing many files as one file and then compressing the size of the file that is used in Unix systems. Another is as self-extracting PCDOS archives. A third is as self-extracting MacBinary II archives created by CompactPro, an archiving program used on Macintoshes and PowerMacs. The fourth is the BinHex format for the self- extracting Macintosh archives. The names of the available archives are
Contents Form Name
-------- ---- ----
C Sources and docs Compressed tar phylip.tar.Z
Pascal Sources and docs Compressed tar phylipp.tar.Z
C Sources and docs PCDOS Self-extracting phylip.exe
Pascal Sources and docs PCDOS Self-extracting phylipp.exe
PCDOS executables PCDOS Self-extracting phylippx.exe/phylippy.exe
386 PCDOS executables PCDOS Self-extracting phylip3x.exe/phylip3y.exe
386 Windows executables PCDOS Self-extracting phylipwx.exe/phylipwy.exe
/phylipwz.exe
C Sources and docs Self-extracting CompactPro phylip.sea.bin Pascal Sources and docs Self-extracting CompactPro phylipp.sea.bin Macintosh executables Self-extracting CompactPro phylipmx.sea.bin PowerMac executables Self-extracting Compactpro phylippmac.sea.bin C Sources and docs Self-extracting BinHex phylip.sea.hqx Macintosh executables Self-extracting BinHex phylipmx.sea.bin You will only want to get PHYLIP in one of the four forms of archive, and generally you will need one of the two kinds of the Sources and documentation files, as the executables archives have essentially no documentation in them. To extract the Compressed tar archives you need to use the utilities "uncompress" and "tar" which are standard on almost all Unix systems. Other mainframe or workstation operating systems may have utilities to do the uncompression and the extraction of these archives. We do not any longer distribute separate executables for Sun, SGI, and DECstation systems, as the C source code of the package compiles easily on those systems using the "make" utility. To extract the self-extracting PCDOS archives, you can simply put them in a (big enough) directory on a PCDOS machine, and execute the archive as if it were a program! Each contains its own extraction program and will extract the separate files from the archive on its own. The self-extracting CompactPro archives were transferred to my workstation using the MacBinary protocol (hence the ".bin" suffix) and with the "binary" mode of ftp set. They should be downloaded to a Macintosh using the "binary" setting (if relevant) and the MacBinary protocol. They can then be extracted using the CompactPro archiver, or ... you can simply put them in a (big enough) disk area on a Macintosh and double click on them. They will then present an opportunity to choose the directory the files go into, and on clicking on the "Extract" button will unstuff themselves into a number of subdirectories and many files. The self-extracting BinHex archives were also made by CompactPro, and then translated into BinHex format. If you decide to use these you must do a binary ftp transfer and then use a program such as Unstiffit Lite to convert the files to self-extracting executables. These then extract when you double- click on them, into a directory that you are asked to choose. We will not describe this option further in the instructions below. How to Transfer the Files by ftp Here is how to use ftp to transfer the archives and how to extract the files from them: 1) Make sure you have enough room for PHYLIP on your system. Most of the archives are compressed by a factor of 2-3, so that you will need enough space on your system to hold each archive (at least temporarily) plus the the files it extracts into. Thus if an archive is 1090k in size you may need 1090k+3270k of disk space to extract it, 3270k being needed permanently. Once you have connected to my machine by ftp, you will be able to see the archive file sizes by issuing a DIR command and can calculate whether you have enough space for the archives you want. 2) Use your local system's version of FTP to connect to my system, which is evolution.genetics.washington.edu. If your system says it has never heard of this address, try the number 128.95.12.41 instead. 3) In response to the "Name" or "Login" prompt, type "anonymous". In response to the "password:" prompt, type your full e-mail address. If you are using ftp from a VAX VMS system or from some Telnet programs you may have to type "user anonymous" to get to log in. It is important that the password you type be a proper e-mail address, preferably your full Internet address. 4) Once logged in, move into the directory "pub" by typing "cd pub". (On some systems the command may instead be "cwd pub".) 5) Move into the subdirectory "phylip" by typing "cd phylip". (On some systems the command may instead be "cwd phylip".) 6) Give the appropriate command to tell ftp that the data will be binary (on my system you type "binary"). If you are moving the files to a Macintosh, make sure that the step that transfers it to the Macintosh uses the "MacBinary" protocol. Some ftp programs such as "Fetch" usually do this automatically but many others require that you choose this option. 7) Look at the above list of archive names and types and decide what you want to get. If you are to get executables, make sure you also will get the source code and documentation archive. 8) To get the compressed tar archive version of the package, tell ftp to get the file phylip.tar.Z (on my system you type "get phylip.tar.Z"). To get the 386 PCDOS executables you will want to get three archives: the source code and documentation archive and two executables archives. Thus you might for example issue the commands: get phylip.exe get phylip3x.exe get phylip3y.exe Similarly for the generic PCDOS version, the 386 Windows version, or the Macintosh executables, you would issue commands to get the source code and documentation archive plus several executables archives. If you are transferring by ftp direct to a Macintosh the Macintosh or PowerMac self-extracting archives, it may be important at this point to ensure that the transfer used the MacBinary protocol. 9) Get out of ftp. (On my system you type "quit") 10a) If you are (say) going to move the self-extracting PCDOS archives to a PCDOS system by a file transfer program such as Kermit, that can now be done, keeping in mind that the archives are binary (not text) files and need to be transferred using the same methods as you would use for an executable program. Similarly, if you are instead using Internet to transfer the archives from one machine to another, use the "binary" mode for the transfer. 10b) (Macintosh CompactPro archives only). You can use a file transfer program to move the CompactPro archives to a Macintosh, but make sure that you enable the "MacBinary" mode which transfers binary files with all their attributes intact. If you use ftp to transfer the CompactPro archives to your Mac, make sure you also have the "image" (or "binary") mode set (as well as the MacBinary, mode so that the files transfer properly. If you use Versaterm to do the transfer to your Mac, make sure that you select "binary" in BOTH the "file" and "kermit commands" menus. To extract the archives simply place them in a disk area that has enough space and then double-click on the file. It will present a dialog box asking where the files should be put. Work your way through the directories, clicking appropriately, until you reach the one where you want them to go. Then click on "Extract". It should self-extract and form a number of folders. 11a) (PCDOS self-extracting archives only): Put each of the two archives in its own directory on a PCDOS system, and simply execute it as a program (i.e., for the file phylip.exe just type PHYLIP, for the archives like phylip3x.exe, and phylip3y.exe that have multiple parts, type the name of each part, PHYLIP3X and PHYLIP3Y). The archive will self extract and a series of files will appear in the directory. At this point you have succeeded. If all files were written you can now delete the archive to save space. 11b) (Tar archives only): If you are on a Unix system you will probably have a utility called "uncompress". Create and new directory and move the archive (say phylip.tar.Z) into it. You can simply issue the command: "uncompress phylip.tar.Z". When the command terminates you will find a file called "phylip.tar". The original compressed tar archive(s) will be gone. Unix systems also have a utility called "tar" that can unpack archives like phylip.tar. The command is most likely: "tar -xvf phylip.tar" (or analogously for other archive names). It will cause the files to be unpacked and placed in the current directory. If you do not have uncompress you will have to use pdtar or zcat instead. If you have pdtar (Public Domain TAR), you can do this by typing "pdtar zxvf phylip.tar.Z" on your system. If you have zcat, type "zcat phylip.tar.Z | tar xvf -". If this doesn't work, consult your local "guru", who may be able to tell you how to uncompress and unpack. 13) REGISTER YOUR COPY. Send electronic mail to me telling me that you have PHYLIP 3.5, which language (C or Pascal) you got the source code in, and which version of the executables you got, that you got these by anonymous ftp. and also tell me: Your name and address (no more than 5 lines total) Your telephone number and electronic mail address (together on 1 line) Name of your computer, operating system, and C or Pascal compiler (all of these together on 1 line) These should start in column 1 without indentation and fit into the required number of lines to make it easier for me to record them in my user database. For example, here is what this material would look like for me:
------------------------------- cut here -------------------------------
Joe Felsenstein Department of Genetics
SK-50 University of Washington
Seattle, Washington 98195 U.S.A.
+1-(206) 543-0150 (work), -0754 (fax),
joe@genetics.washington.edu
DECstation 5000/200 and 5000/125 with Ultrix 4.2 and DEC Ultrix RISC C compiler
------------------------------- cut here -------------------------------If you can do it in that format you will save me a lot of typing and editing. My email addresses are: Internet: joe@genetics.washington.edu joe@evolution.genetics.washington.edu joe@128.95.12.41 and my phone numbers are: Work: (206)-543-0150 Home: (206)-526-9057