Hi,

Does anyone know how I can modify the command line parameters in needleall to output query coverage? So far my code below only gives me values for Identity, similarity, gaps, and score. 

    needleall -asequence proteins_f1.fa -bsequence proteins_f2.fa -outfile needle_results -aformat pair -gapopen 10 -gapextend 0.5

Thanks very much.

A global alignment does not give a coverage. "It will always try a coverage of 100%", a global alignment will try to align the **full** sequence in the best possible way.