compare subsets of sequences in multiple alignments

Question

[alessandrotestori7]

Hi! I am interested in inferring whether a subset of sequences extracted from a multiple alignment has several sequence peculiarities (e.g.: a hyper-conserved base at some position). Are there any tools which take as input the alignments? Alternatively, which statistics should I use? Thanks!

Answer 1

[Michael]

Jalview can do this. You can also select a subset of rows and colums and compute a new alignment on the fly.

Answer 2

[Suzanne]

Jalview is a free protein and nucleic acid sequence alignment visualisation software that can compare subsets of sequences in multiple alignments. I suggest you check out the video on 'selecting residues, sequences and columns of proteins' (https://youtu.be/WUTlDJO9xxQ). This is one video in Jalview YouTube 'selecting and editing sequences' playlist (https://www.youtube.com/playlist?list=PLpU3VZmUmrT27N2Uy32qszCOoznvN-07N). The program can be launch from http://www.jalview.org/.

[alessandrotestori7]

Thanks for the detailed instructions.