Multi-Sequence Alignment Tool

Question

[Daniel]

Hello,

I am trying to figure out which multi-sequence alignment tool to use, and it has been quite difficult to find papers/threads about the tools out there and their use-cases. The problem is also that many of these tools are from the early 2000s, and so I want to make sure I'm not overlooking anything modern by using them. The most helpful material I found so far was here (https://mafft.cbrc.jp/alignment/software/about.html), which describes the merits of MAFFT, and this paper https://link.springer.com/protocol/10.1007/978-1-0716-1036-7_17#Sec2, which implied that there have not been major recent developments. All guidance would be very much appreciated, Thank you!

Answer 1

[Mensur Dlakic]

MAFFT is a fine choice. So is Clustal Omega. Unless you have very large alignments (> 10,000 sequences), MUSCLE works fine as well.

[Daniel]

Thank you so so much!