| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| README.txt | 2014-05-07 | 2.3 kB | |
| diCal-v1.3.tar.gz | 2014-05-07 | 602.1 kB | |
| diCal-v1.2.tar.gz | 2013-08-20 | 593.0 kB | |
| diCal-v1.1.tar.gz | 2013-06-17 | 494.0 kB | |
| diCal-v1.0.tar.gz | 2013-06-11 | 493.4 kB | |
| Totals: 5 Items | 2.2 MB | 0 |
Copyright (c) 2013, Sara Sheehan, Kelley Harris, and Yun Song License: FreeBSD (Berkeley Software Distribution) USAGE: Please refer to the accompanying manual (manual-v1.3.pdf) for usage instructions and contact information. Questions and suggestions for improvement are appreciated, please include "diCal" in the subject line of your email if possible. HISTORY: ------v1.3------ NOTE: v1.3 has been updated -example parameter file now specifies that *theta* should be used for the mutation rate, not mu -includes an example parameter file suitable for humans -Fixed bug that caused some slightly super-linear runtime in the number of discretization intervals. -Added option for printing expected coalescent events in each time interval (note this is not linear in the number of discretization intervals). -Also note that printing a decoding will not be linear in the number of discretization intervals. -Now computes a suggested JVM memory flag (-Xmx) based on the input data. -Other code clean up for consistency. ------v1.2------ -Supports VCF file format (use the provided converter to create a simplified VCF). -Implements a decoding algorithm and corresponding M-step updates that are linear in the number of discretization intervals. -The adaptive parameter pattern method is no longer supported since it does not work well with the linear implementation (might be updated in the future). -Some of the input flags have changed to be more intuitive and compatible with the PSMC (see manual-v1.2.pdf). -General refactoring and code cleanup, added unit tests. ------v1.1------ -Supports missing bases (N/n). -Supports multiple chromosomes/scaffolds per individual. -Updated decoding format and additional decoding option. -Small change to the emission computation for numerical stability. ------v1.0------ -Initial release. Notes: -The Java Matrix Package (Jama-1.0.2.jar) was unavailable during the lapse in U.S. government funding. It is currently available as described in the manual, but it can also be found on Google code at https://code.google.com/p/relativelayout/downloads/detail?name=Jama-1.0.2.jar&can=2&q=. -The files diCal.tar.gz and diCal-2013-06-10.tar.gz have been renamed to diCal-v1.0.tar.gz and diCal-v1.1.tar.gz, respectively.