A new release is now up. There are a few changes and improvements as well as a few more compatibility improvements with ms.
The first major improvement is that condition on the number of segregating sites now works. This is the -s option in ms and I simply forgot to put it in. Using the -s option will tend to use more memory and be a little slower. This trend will get worse with deeper highly recombinant trees. However its not a huge difference in most cases of interest.
The next big improvement is the addition of more boundary conditions. That is you can now set the frequency at a
particular time or in a particular deme rather than just fixation time. This option is just the old -SF
option with more arguments. As an example, we want to condition on the frequency in deme 1 to be 0.5 at a time
of 0.01 pastward:
msms -ms 20 1000 -s 100 -SAA 1000 -SaA 500 -N 10000 -SF 0.01 1 0.5
If I want to condition on the total frequency of the beneficial allele in all demes at sampling time to be 0.8
I would use the following:
msms -ms 20 1000 -s 100 -SAA 1000 -SaA 500 -N 10000 -SF 0 0.5
So the form is -SF fixationTime for a the fixation time. -SF time freq to condition on a
frequency or -SF time deme freq for the frequency in a given deme.
Another thing that has changed is the first line of output is now the full command line. Note that for some ms parsing tools you will need to be careful to use msms options last. We also now have a -seed switch and we write out the seed value on the second line. This is a 64 bit number so we used hex. But the -seed option can use hex(prepend with "0x") or decimal.
Unfortunately none of the new improvements have made it into the manual yet. This is next along with some more examples.
Finally some mac users had problems downloading new versions because Firefox cached the download. To avoid this problem we will now include the version number in the link and file names.
Despite the lack of "news" there has been plenty going on behind the scenes. I have added some links to the mailing lists and forums with the getting help page in the menu. We are working on an ABC mode for msms that integrates with the ABCtoolkit. There are some other new features coming soon for summary statistics output that make using msms in a pipeline much easier. This is just some of the things that are "coming soon".
The manuscript has been accepted in Bioinformatics. The link to the application note is here.
We have added some performance comparisons to the manual against ms and against itself with and without selection. Generally speaking msms is much faster for high recombination rates even with neutral models.
Also some mailing lists have been set up, we encourage all uses to subscribe to the news list. The other lists can be found here. The main sourceforge page is can be found here and there are forums available for help.
There were some minor bugs that have been fixed. These resulted in lockups in odd situations. Also, some more internal rescaling was fixed to be more consistent.
Finally, some simple tests were added. These tests compare mean and variance of tree length, tree height and segregating sites statistics with known correct values. I have found that these statistics are quite discriminating when it comes to finding bugs. Currently we are comparing test vectors with ms, however other programs such as SFSCode will be used for test vectors in the near future.
Please notice that these tests are statistical in nature. Thus, we expect it to fail on occasion by chance alone. Inspect the values displayed in the output and rerun the tests. Generally different tests should fail each time, or none at all. Remember this is compounded by the multiple test problem. That is each test vector results in 6 tests. So even with just 7 test vectors, we have a total of 42 tests. Hence, a p value of 0.05 would result in 2 failures each time. In this case, we simply choose a threshold that's good for discovering bugs while not failing every time.
In order to run the test, under Mac and Linux, there is a simpleTests
script in the bin directory. Under windows use the following command
line:
java -cp lib\msms.jar at.mabs.testing.BasicTests
There was a regression in the recombination code when using selection. Please update to the latest version.
A new version has been released today. This is a bug fix release, and it fixes some internal scaling issues when selection is used. I do believe this will not affected results much, the error should be second order only at worst and would only show up with very small population sizes and very small selection parameters.
However fixing this scaling means that I needed to add a lot of 2's to the code base. I have double checked everything and expanded my tests to catch errors. I did not find any. But code has a habit of hiding bugs well. So if something changes a lot between this version and the last, I probably missed a 2 somewhere.
Today the final version 1.0rc release candidate is available. This should be more stable and even a little faster than previous releases. We also have the prepacked archive for easier installation with a Mac, Linux and Windows launcher. Note you will need to have at least java version 1.6 (some times called 6) as per previous versions. This can be a little tricky for Macs, however we hope the instructions on this web page and in the manual are clear enough.
Assuming no big changes need to be made, this should roll over to a full version 1.0 with a public git repository and full developer documentation in a few weeks. Please report all bugs both in the application and documentation and even in the web site. But please note my comments about the site below
What I really want is a fairly easy Content Management System for the web site that would include a few extras from what we have right now. For example, a mailing list, a wiki and forums would be nice. Suggestion are welcome. Note that googgle source is nice, but lacks git support. Sorceforge has serious issues with its very kludgy forums, and last I checked they don't offer a full CMS and wiki.
In the mean time I will probably set up a google groups just for the email list. Feedback is welcome.
With only days away till the version 1.0rc release, things are happening pretty fast. All user documentation will be done. However, some of the developer documentation will still need some work. At this stage, this is the web site we shall use which is all about very low maintenance. But if need be, we will migrate to a wiki based site. Mailing lists shall be set up shortly.
The current plan is to release a version 1 release candidate by March 10th. This would also be a clean slate on the git public repository. The license will most likely be GPL 3, but I am double checking with one or two of the packages that I use. In particular, I use args4j which uses an Apache type license. I don't think this will cause problems as I have not modified args4j in anyway.
The documentation will also be released at the same time.