Revision history for Bio::fastAPD 1.10.0 04/08/2015 This is a major release with substantial changes. This release is not backwards compatible with scripts designed for previous versions. Our method for rapid calculation of APD remains unaltered, thus APD results from previous versions should be identical to those calculated with the current release. A fix has been applied to correct standard error estimates which were determined to be incorrect under certain conditions. Major Changes: 1. The apd_by_pos() function has been removed. Although this alternative method for rapid calculation of APD was previously provided for the sake of comparison with our method, it was removed from the current release due to the absence of a robust mathematical justification. 2. The 'gap_gap' option for missing data handling in the apd and standard error calculations has been removed. Thus the current options for missing data are pairwise deletion (base_base or gap_base) and complete deletion (complete_del). 3. The main function calls have been updated to reflect the changes described above. The rapid APD and standard error calculations are now performed as follows: $fastAPD_obj->apd('gap_base'); $fastAPD_obj->std_err('gap_base'); 4. It was determined that the standard error estimate was incorrect when performing a 'complete_del' analysis on datasets in which positions may consist of an insertion in a single sequence (thus gaps present in all other sequences). This is also relevant for calculations involving thresholds for missing data (N's, gaps, or ragged ends). This has been corrected in the current version. 5. The testing and example scripts have been appropriately updated. 1.08 12/14/2014 Added META.yml 1.07 12/10/2014 Added LICENSE file, as well as MYMETA.json and MYMETA.yml. 1.06 12/09/2014 Removed developer tests. 1.05 12/08/2014 Included inc/Module/Install. 1.04 12/08/2014 Adjusted test.t for new output from freqs(). 1.03 12/08/2014 Fixed namespace in 00-load.t and altered output format of freqs() in fastAPD.pm. 1.02 12/04/2014 Propagated new namespace throughout module (Changed fastAPD to Bio::fastAPD). 1.01 12/03/2014 Minor bug fix for example_script.t. 1.00 12/02/2014 First version released.