To Run Mesquite

To run Mesquite, you need Java installed. Mesquite now runs only on Java 1.4 and
higher. We suggest Java 1.6 on Mac OS X, Java 1.7 on others.

Once Mesquite_Folder is installed, you can start Mesquite as follows:

==================
Mac OS X
There are 3 ways to start Mesquite under OS X:

1. Default: Double click Mesquite[500GB].app, Mesquite[1GB].app, or

Mesquite[2GB].app, depending on how much memory you want to give to Mesquite.

3. Or, to adjust how exactly Mesquite starts, including memory allocation:

Run Mesquite by double clicking the file Mesquite_Start_Script.command. If double
clicking this file does not start Mesquite, select the file in the Finder, choose
Get Info, and change the "Open With" to "Terminal.app", which is in
/Applications/Utilities/

To give Mesquite even more memory, open the file with a text editor and edit the
line:

java -Xmx500M -Xss2m -Djava.library.path=lib -cp . mesquite.Mesquite

The part -Xmx500M indicates how much heap memory to give to Mesquite in general.
With more heap memory Mesquite can handle more trees, bigger matrices, bigger
charts, and so on.
The part -Xss2m indicates how much stack memory to give to each thread. With more
stack memory, Mesquite can handle bigger trees, e.g. more than 5000 taxa. To be
able to handle 10000 taxa, you may need to increase this to 4m.

If you change these settings, make sure you don't introduce any spaces.

Here are some example configurations:

java -Xmx1000M -Xss4m -Djava.library.path=lib -cp . mesquite.Mesquite

This can handle big matrices and trees, but you'll probably need at least 2 GB
memory in your computer to use it conveniently.

java -Xmx3000M -Xss4m -d64 -Djava.library.path=lib -cp . mesquite.Mesquite

This gives much memory to Mesquite, but 3000 MB (= 3 GB) memory exceeds the ability
of 32 bit Java. For that reason the command -d64 was added, to indicate you want
to use 64 bit java. This is available only on intel-based Macs with Core 2 Duo or
better processors and updated versions of Java.

==================
Windows

There are 3 ways to start Mesquite under Windows:

1. Default: use the installer and double click one of the executable icons
(Mesquite[500MB].exe, Mesquite[1GB].exe, Mesquite[2GB].exe), depending on how
much memory you want to give to Mesquite.

2. Or, to adjust how exactly Mesquite starts, including memory allocation:

Run Mesquite by double clicking the file Mesquite_Start_Script.bat. To give
Mesquite even more memory, open the file with a text editor and edit the line:

java -Xmx500M -Xss2m -Djava.library.path=lib -cp . mesquite.Mesquite

The part -Xmx500M indicates how much heap memory to give to Mesquite in general.
With more heap memory Mesquite can handle more trees, bigger matrices, bigger
charts, and so on.
The part -Xss2m indicates how much stack memory to give to each thread. With more
stack memory, Mesquite can handle bigger trees, e.g. more than 5000 taxa. To be
able to handle 10000 taxa, you may need to increase this to 4m

If you change these settings, make sure you don't introduce any spaces.

==================
Linux etc.

Run Mesquite by double clicking mesquite.sh or running mesquite.sh from the command
line like this:
./mesquite.sh

Alternatively, run it from the command line by cd'ing into Mesquite_Folder and then
giving a command like this:

java -Xmx500M -Xss2m -Djava.library.path=lib -cp . mesquite.Mesquite

The part -Xmx500M indicates how much heap memory to give to Mesquite in general.
With more heap memory Mesquite can handle more trees, bigger matrices, bigger
charts, and so on.
The part -Xss2m indicates how much stack memory to give to each thread. With more
stack memory, Mesquite can handle bigger trees, e.g. more than 5000 taxa. To be
able to handle 10000 taxa, you may need to increase this to 4m

Here are some example configurations:

java -Xmx1000M -Xss4m -Djava.library.path=lib -cp . mesquite.Mesquite

This can handle big matrices and trees, but you'll probably need at least 2 GB
memory in your computer to use it conveniently.

java -Xmx3000M -Xss4m -d64 -Djava.library.path=lib -cp . mesquite.Mesquite

This gives much memory to Mesquite, but 3000 MB (= 3 GB) memory exceeds the ability
of 32 bit Java. For that reason the command -d64 was added, to indicate you want
to use 64 bit java.