CodonCode Aligner Forum

Hello, The updates to aligner's scripting have made it much more useful. However, does aligner allow any method to fully automate the execution of aligner scripts via command line? For example, DNAstar allows you to execute a SeqMan script from the command line by adding the script as an argument af...

I am trying to script some basic sequence processing tasks. I would like the end-product of the script to be an aligner project, which is why I am trying to use aligner, not phred/phrap. Most commands seem straightforward, however I have a couple questions: With all assembly commands, can i specify ...