MUSCLE and Trees
When you want to look for conserved regions in your DNA sequences, reach for MUSCLE. It’s fast and offers better accuracy than many other multiple-sequence aligners. It’s easy to use, and with Sequencher Connections, not only do you get to see the aligned regions, you can also see your results in rectangular or circular tree format.
You can set up several MUSCLE runs on the same group of sequences with each analysis (or channel) set up to use different parameters. Do you want to keep different sets of data together but run the same MUSCLE parameters on them? Add them to the same Connections session because each row in the session can contain a different group of sequences. MUSCLE runs on the different channels and rows and can then be compared, giving you a unique perspective on your data.