sfs_code / News: Recent posts

Dear SFS_CODE'ers,

I've posted an update to SFS_CODE to the project page. There are several updates, including bug fixes and new features. You can read about them in the Release Notes pasted below.

Let me know if you have any questions.

Happy simulating!

Ryan

* CURRENT RELEASE: *

DATE: 2015-08-15

NEW FEATURES:

Generally much faster.  I made a few improvements to the way data structures are handled.... [read more](/p/sfscode/news/2015/08/sfscode-update-2015-08-15/)

DATE: 2014-07-19

This release includes two primary bug fixes, a couple of additional features, and a major efficiency optimization.

BUGS:

Bug 1: Time to fixation conditional on fixation. This should affect only simulations where a large number of bases are simulated (e.g., 1Mb or larger), and you are looking at the time to fixation conditional on fixation for mutations in a small simulated chunk (e.g., 1kb). This could arise when you are interested in a locus surrounded by deleterious background, or if you are simulating an exome. The previous version reported fixation times that were too large. This did not impact segregating variants.... read more

There is a new version of SFS_CODE available for download from sfscode.sourceforge.net. There is a new option, and a couple of bug fixes. In the previous version of this post I regretfully forgot to thank the people who helped me discover the bugs.

NEW OPTION:

• More of a sub-option. This is motivated by some simulations Lawrence Uricchio (grad student in the lab) has been doing under a recurrent hitchhiking model. SFS_CODE now allows more flexibility for the mutation rate variation across loci. You can now specify the mutation rate at a specific locus directly, rather than relying on SFS_CODE to draw the rate from a given distribution.
  --rateClassLoci (-v) [L <locus> <rate>]</rate></locus> [ [P <pop>] <n_classes> <alpha>]</alpha></n_classes></pop>... read more

Updates:
See documentation for details, but here is a brief description.

• SFS_CODE now supports various equilibrium nucleotide frequencies using the --b
  aseFreq (-q) flag (which can be set to change over time).
• When simulating CpGs using --substMod 3, there is now a separate parameter for
  the transition/transversion bias at CpG sites.
• Added --substMod 6, which is the general time reversible (GTR) nucleotide subs
  titution model. This works in conjunction with --baseFreq.... read more

I have made minor updates to SFS_CODE, but they have come at the benefit of a considerable decrease in computation time. As an example, the previous version took about 36 seconds to simulation 1MB in a population of size N=250. The current version takes about 24. For N=500, it took 90s, now it takes 61s. I will update the table and figures on the performance tab of the webpage when I have time to run all those simulations.... read more

SFS_CODE has been updated to allow for gene conversion (with the option of being GC-biased). This involved quite an overhaul of the way recombination is simulated. I’ve gone ahead and compared SFS_CODE to ms again, and everything that was on the Comparisons and Expectations tab still checks out. I added an additional description regarding the comparison of the two programs with gene conversion (and the parameter conversion that you have to do to get them to match) in the documentation. I don’t know of any other programs that simulate biased gene conversion, so I can’t do any standard comparisons, just my own semi-rigorous bug checking.... read more

Announcing the first release of SFS_CODE!! The program can now be downloaded from the project page.

I have also updated the project website. More on the way! Coming soon:

1. comparison of neutral SFS_CODE simulations to the standard coalescent (ms).

2. comparison of SFS_CODE simulations with selection to expectations under the Poisson Random Field.

Happy simulating!!

Ryan

The future home of the SFS_CODE source has been posted at sfscode.sourceforge.net.

After defending my PhD thesis on December 6, I will update the website, and post the source code.