Jane

F.A.Q

If you don't find the answer to your question here, don't hesitate to email us.

Questions

  1. When I try to run large trees, Jane crashes.
  2. Jane won't even start.
  3. How do I make Jane run faster?
  4. I saved the results of my statistics run as a CSV file, but when I try to save it, Excel warns me that I might lose some of my data.
  5. I saved a solution or histogram as an image, but when I view it the background is black. Wasn't it white earlier?
  6. Can I still get earlier versions of Jane?
  7. How do I contact you?
When I try to run large trees, Jane crashes.
This is almost certainly because Java ran out of memory. The default setting for the Windows, Macintosh, and Linux distributions is 512 megabytes of memory. If you need to use more, try downloading the platform independent jar file from the downloads page and then run java -Xmx1g -cp Jane.jar edu.hmc.jane.gui.Design from the command line. Back to Top
Jane won't even start.
Try downloading the platform independent jar from the downloads page, and then run java -cp Jane.jar edu.hmc.jane.gui.Design from within the folder that you put the JAR in. Back to Top
How do I make Jane run faster?

There are a few things. Jane is designed to take advantage of multi-core processors, so if you upgrade to more cores, you'll get an almost linear performance improvement. (Eg. if you go from a single core processor to a dual core processor, Jane' speed will approximately double.)

If you are currently running a 32-bit JVM (Java Virtual Machine), you can get an approximately 2.5-fold performance increase by switching to a 64-bit JVM. (If your computer is old, this may require buying a new one, as the 64-Bit JVM will not run on some older computers.) Here is how to do that on Windows.

First, check to see which version of the JVM you are running. You can do this by simply running Jane' GUI or command line interface. If you don't get a warning, you are already using a 64-Bit JVM and don't need to do anything. Otherwise, continue with these instructions.

Download the 64-bit JVM from here. Specifically, choose to download the JDK and not the JRE. Then agree to the license agreement and select Windows x64 from the options given. Once you have downloaded the file, install it.

After the install finishes, try running Jane again and check to make sure that the warning is gone. If the warning is still there, ask for help from your IT department. One troubleshooting step you might try is to make sure you do not have a 32 bit JDK installed (the 32 bit JRE is fine). You can check whether it is installed using the add or remove programs control panel feature and looking for programs beginning with "Java".

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I saved the results of my statistics run as a CSV file, but when I try to save it, Excel warns me that I might lose some of my data.
Don't worry. What Excel is saying is that if you choose to re-save the file in the CSV format, rather than the Excel format, some minor things like font, formatting (bold, italics, etc.) might be lost. Your actual data will be fine. If you wish to ensure you retain the formatting as well, you should use the save as feature in Excel to save it as a .xls or .xlsx file. Back to Top
I saved a solution or histogram as an image, but when I view it the background is black. Wasn't it white earlier?
When you save the solution, it is saved with a transparent background. Some programs interpret the transparency as the equivalent of black. Try opening the solution in Firefox or Photoshop, and you will see that the background is still clear. Back to Top
Can I still get earlier versions of Jane?

Jane 3 contains a number of features not present in Jane 2 such as failure to diverge events and time zone support. In addition, the randomization method used in statistics mode did not work correctly in Jane 2 and has been fixed in Jane 3. Jane 3 also tends to be faster on larger trees (50 tips or more) while Jane 2 is faster for smaller trees. Both Jane 3 and Jane 2 are available at the download page.

While both Jane 3 and Jane 2 demonstrate significant speed improvements over Jane 1, contain multiple bug fixes, and produce the same (and sometimes better) quality solutions, you are free to download and use the original version of Jane from the Jane 1 website.

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How do I contact you?
You can get our email address by clicking here. Back to Top
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