Merge branch 'master' of https://github.com/chilleo/ALPHA

Author: chilleo

README.md

@@ -7,6 +7,7 @@
       - [MS Comparison](#ms-comparison)
       - [D-statistic](#d-statistic)
       - [Generalized D-statistic](#d-gen-statistic)
+      - [Smooth Winds](#smooth-winds)
     - [Output Files](#output-files)
 - [Installation](#installation)
    - [Mac Installation](#mac-instructions)
@@ -183,6 +184,13 @@ Meta:
 
 Finally, if you have already generated and saved a DGEN statistic, simply launch the dgen tool and select an alignment you wish to analyze. Then select the "Load Previously Generated Statistic" checkbox along with selecting the statistic file itself at the location it has been saved on your computer. Then set the window size and offset and optionally change the alpha significance cutoff parameter. To see a graphical output of a plot of the generalized D value versus the windows along the alignment, simply check the "generate plot" checkbox.
 
+
+#### Smooth-Winds
+
+UPDATE 4/44/19:
+
+The Smooth Winds page has been created with an accompanying command line script. This documentation will be soon updated alongside a companion publication. Thank you for your patience in the mean time.
+
 ### Output Files
 
 All output files are automatically saved in various folders in ALPHA. Windows that are created by RAxML are outputted into the “windows” folder, and are saved as “window0.phylip”, “window1.phylip”, etc. Files outputted by running RAxML are found in the “RAxML_Files” directory. When bootstrap analysis is chosen these files are saved under “RAxML_bestTree”, “RAxML_bipartitions”, “RAxML_bipartitionsBranchLabels”, “RAxML_bootstrap”, and “RAxML_info”. When bootstrapping is not chosen these files are named “RAxML_bestTree”, “RAxML_randomTree”, “RAxML_result”, “RAxML_log”, and “RAxML_info”. Each of these files has “.0”, “.1”, “.2”, etc. extensension corresponding to the index of the window that RAxML was run on. All graphs and images are automatically saved into the plots folder under the name of the image.