This folder has an alpha release of the program Threshml, from PHYLIP 3.7a. That version of PHYLIP is not yet released as other programs are not in a releasable state yet.
My paper describing Threshml is:
|Felsenstein, J. 2012. A comparative method for both discrete and continuous characters using the threshold model. American Naturalist 179: 145-156.|
The files here include a documentation web page file, threshml.html which explains the options and use of Threshml.
They also include some pieces of the source code:
|threshml.c||The main Threshml program|
|cont.h||a header file for them|
|phylip.c||more widely-used PHYLIP functions|
|phylip.h||the main PHYLIP header file|
|Slist.h||... and their header file|
|ml.h||header file for likelihood|
You mostly do not need to worry about these files once Threshml is compiled.
In addition there is a Unix/Linux Makefile for compiling Threshml:
A zip archive of the source code, executables, and the
documentation files is also available. It is called threshml.zip
It may be the easiest file to download to get everything. It can be downloaded at this link.
We have also included several executable files compiled for various systems. The relevant one could be copied to another folder, and renamed "threshml". On some systems you might also need to give that executable file "execution permission" with a command such as (for Unix, Linux, or Mac OS X) "chmod +x threshml"
Here are the executables available now:
|threshml.linuxi64||Intel- or AMD-compatible 64-bit Linux executable|
|threshml.linuxi32||Intel- or AMD-compatible 32-bit Linux executable|
|threshml.exe||32-bit Windows executable|
|threshml.osx||Mac OS X universal executable Intel or Powermac|
For the moment the Mac OS X executable needs to be run from a Terminal window by typing "threshml" or by typing "./threshml" We do not yet have a version available that will run by clicking on an icon.
The Windows executable can be run by double-clicking on its icon.
Note that some systems will not be happy downloading an executable from elsewhere and allowing it to run on your system. In these cases you might be able to do the compilation locally, using the instructions below.
For Linux or Unix systems, or for Mac OS X systems you can compile an executable of your own by following these steps:
make threshml -f Makefile.unix|
|make clean -f Makefile.unix|
Important: you don't need to do any compiling if you can use one of the precompiled executables described above. There is then no reason to compile.
For Mac OS X systems, the above instructions will work. However if you want to compile a universal executable, rather than one which will work only on your processor, you need to edit the Makefile.unix file, and remove the initial "#" character from the special CFLAGS line that is for OSX compiles, and instead place that character on front of the CFLAGS line which is for the GCC compiler. Then do the compilation as described above.
For Windows systems we have a line in the Makefile.unix that can be used with the CygWin GCC compiler to compile the program. If for some reason you cannot use our precompiled Windows executable and want to compile one of your own, you need to edit the Makefile.unix file, and remove the initial "#" character from the special CFLAGS line that is for CygWin Windows compiles, and instead place that character on front of the CFLAGS line which is for the GCC compiler. Then do the compilation as described above.
Department of Genome Sciences
University of Washington
Seattle, WA 98195-5065