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.