Definition of 'alignment score'

[jvivian-atreca]

Thank you for the great program Jeff. I noticed the documentation doesn't provide a formal definition for the returned "alignment score." Can you clarify how this score is computed?

[Jeff Daily]

Here's a quote from perhaps midway through my README.

A good summary of the various alignment algorithms can be found courtesy of Dr. Dannie Durand's course on computational genomics here.

Hope that helps.

[jvivian-atreca]

Ah I missed that. Thank you @jeffdaily .