Output machine-readable alignment

[wiedenhoeft]

I would like to submit a feature request: So far, TRF outputs the query sequence to the .dat file or stdout. However, the alignment only appears in the HTML file. Parsing it out is possible, but error-prone.

Would it be possible to add two columns to the non-HTML output corresponding to the two alignment lines, with dashes (-) for indels and some separator (like | or ,) to demarkate the individual blocks that are separated by spaces in the HTML?