I have the consensus sequence for 48 strains that I have mapped and aligned to a reference using CLC. They are each of approx 3Mbp (about 100bp difference in lengths between the sequences). I am trying to perform a time divergence analysis, but before that I need to format my sequences so that recombination has been considered and the alignments are all of the same length.
I would like to know if there is any software that would perform a multiple sequence alignment across the 48 strains, and remove positions where there is little or no coverage in at least one of the 48 strains, and that handles indels.
I would like this software to produce 48 sequences of equal length so that they may be fed into other software such as Gubbins (detect recombination), then Beast (time divergence). I have tried to use GBlock, but this software requires sequences to be of the same length.
I look forward to hearing your response and ideas.
Thank you and kind regards,
Thank you arnstrm, this worked a treat!
Hi I tried doing the same thing except got a segmentation fault (11) error