The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. Others can be specified.
Users can provide their own data files in their own directories.
Notes needle is a true imple,entation of the Needleman-Wunsch algorithm and so produces a full path matrix. It therefore cannot be used with genome sized sequences unless you've a lot of memory and a lot of time. 1-44 Addison Wesley. Warnings needle is for aligning two sequences over their entire length. This works best with closely related sequences.