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compare subsets of sequences in multiple alignments

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!

sequence alignment genome
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updated by Suzanne Suzanne • written by alessandrotestori7 alessandrotestori7

2 answers

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

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written by Michael Dondrup Michael Dondrup

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/.

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written by Suzanne Suzanne

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