After carrying out automatic alignment on a set of proteins (e.g using MAFFT, Muscle, ClustalOmega), it is often necessary to manually edit the alignment.
What is the basic principle behind such manual editing? What should one be looking for in the MSA to manually correct?
Are there any tutorials or articles on how to carry out such manual alignments?
The data set may be very large (I have 1520 proteins). Will I need to visually inspect the entire dataset? Can a script (e.g python) be used to look for errors and also to 'manually' edit those errors? Or are there any bioinformatics software that can suggest what sites need manual adjustments?
P.S: I am new to bioinformatics research and manual alignment is something I hear everyone say they did but no one explains how they did it!
