I'm trying to align two DNA sequences with EBI's Exonerate sequence alignment tool. When trying to do
affine:overlap, the program exits with generating the following error message
**"** FATAL ERROR **: Cannot perform heuristic alignment using non-local model"**
Running the program with "--exhaustive y" switch , as shown below, stops it from exiting. However, no alignment is produced.
exonerate --model affine:global --exhaustive y -q ./query_seq.fasta -t ./target_seq.fasta
ungapped:trans etc. are working fine. The two input sequences are of different lengths. I'm not sure if they have to be of same length if I've to do
affine:overlap,though I guess not.
Thanks for your answers