When submiting or adding a script to this database, please add an entry to the table_of_contents.csv file. If you do not believe there is an applicable directory for your script in the database feel free to create one, but make sure it is meaningfully distinct from those that are already present.
Included herein are all of the scripts submitted by the Gogarten lab for public use. These include scripts written by both present and past lab members (if you are the author of an older script contained here, please contact us by email, and we can remove it).
Scripts are organized generally by the task they are associated with (for more detailed descriptions, see comments below).
Scripts that:
-Edit file names
-Rename or reformat file content
-Extract information
Note: These scripts should be applicible to more than just one specific analysis.
Scripts that:
-Create databases
-Search databases
-Reformat databases
Scripts that:
-Align sequence files
-Edit alignments
-Parition alignments
Scripts that:
-Construct phylogenies
-Edit phylogenies
Scripts that do not fit the above categories. Please provide a proposed category in the notes section.