Hi all !
I'm looking for a method to select / visualise quickly the most related peptide sequences from a list of aligned sequences.
I have a group of 1,500 peptide sequences that I have aligned with a multiple sequence alignment software.
I cannot obtain a alignment score (or pairwise identity %, or Identical sites %) for each pair of sequences, and obviously I cannot align manually all the possible combinations of sequence pairs (i.e sequence 1 with sequence 2, 1 with 3, 1 with 4... 1 with 1500, 2 with 3, 2 with 4...), in order to obtain a score for every pair of sequences.
So I'am looking for a way to visualise subgroup of close sequences among my 1,500 peptides.
I'm thinking about using a tool to build phylogenetic tree, but I'm not a pro. in this field and I don't know which matrix to choose and how interpreting the tree (Do 2 similar sequences be under a same node, or have similar distances ????)
I'm totally lost ! If someone is used to work with this tool, his/her explanations would be very helpful