dist.seqs screen.seqs and distances in generell

a very basic thing probably I have been thinking about:
when I measure the nucleotid distances using a multiple sequence alignment, and I have a lot of variation in size and overlap of the sequences- I do use screen.seqs to make the overlap as big as possible, right? When the distances are now calculated - are always just the distances between " existing" nucleotides calculated and the regions which do not overlap are disregarded? Or are the also used in the calculation?

Means do all my seqs need to be exactly the same length in order to have a good distance measurement? If so - I have to sacrifice a lot of the sequences …:(?

Thanks a lot for help -

Yep. The distances are between the existing sequences. This is actually critical as the gene does not evolve at a uniform rate along its length. Including varying lengthed sequences or sequences that don’t overlap results in a comparison between apples and oranges. You can learn more from this…