Anyone knows if there is an implemented function in biopython to calculate gap windows and their length in a multiple sequence alignment. I found a module (http://biopython.org/DIST/docs/api/Bio.Align.AlignInfo-pysrc.html) to calculate the consensus sequence but it do not allow to set that 1 gap in any sequence should give an output of a gap in the consensus. My input is a Clustalw alignment.
Seq1 AAATCG-- Seq2 ---TCGAA Seq3 -AATCGAA Seq4 -AATCGAA ***
consensus would be: ---TCG--
desired output: gap windows = 2