That was 47 years ago, as I remembered those researching days fondly, gently watering the roots of the orange tree in my yard that stared thankfully at me.
Hi, I have 10-50 whole chloroplast genomes from ncbi to align, of a single species plus a nearby outgroup. I've tried running MAFFT with default parameters, and while it finishes in a few hours with no errors, the resulting multiple sequence alignment is garbage -sequences are nearly double the original length and full of dashes. I don't have any experience in plant genetics, but I'm wondering if this is because of the two inverted repeats found in the chloroplast genome, or something similar regarding low complexity regions. All the literature just says "we aligned them using mafft" with no further details. Also tried muscle but it's really slow.
Does anybody know how to do this? Thanks :)
Edit: I should have specified I need a multiple sequence alignment.
Hello! 2-3 weeks ago I did a chloroplast isolation experiment with my classmates. We are responsible for writing reports about our experiments and there was a question in this experiment's report saying that 'For high quality chloroplast isolation, it is recommended to keep the spinach leaves in the dark for at least 2 days. What could be the scientific background of this approach?'. I searched up on the internet but i could not find any solid answer.. Thanks for your reply.
Wouldn't the fact that cells had to capture chloroplasts and different cells captured mitochondria mean Eukaryotes evolved twice?
