Background: I am trying to build a tree of sequences (non-coding DNA) I obtained in my lab, along with appropriate similarly related known sequences and outgroups. I am using MEGA-- I understand the process of inputting sequence files, and basic concepts of using Clustal W (or Muscle) to align the DNA nucleotides. I also know downstream, I will be using MEGA for determining the ML model of best fit,and creating a ML tree with bootstrapping.
I also am new to this so correct me if wrong -- but after inputting sequence files in MEGA, I need to either 1) align by Clustal W/Muscle and then manually align; or 2) submit the unaligned file to a program that will check it for quality of sequences/columns and then use the edited version for tree building.
My question: Once my sequences are in MEGA, what is the best way to manually align ( after Clustal W) /ensure for quality sequences and regions? I understand this must be done before moving forward in the tree process. I've read Guidance is good for this, but after trying to use it I couldn't download the files in an appropriate file form. Any suggestions on appropriate programs (free if possible) would be appreciated!!! Thank you!