What is the best tool for generating Multiple sequence alignment (MSA) of fasta sequences ?

Question

[sunnykevin97]

HI, Could anyone suggest me the best tool, for performing multiple sequence alignment among fasta sequences. Should generate output in MAF (Multiple alignment format) ?? The input --> fasta format The output --> in MAF (Multiple alignment format) thanks!

Answer 1

[Jean-Karim Heriche]

Defining which tool is best depends on what criteria are important. Since we don't know what these important criteria are for you, we can't give an answer in terms of best tool. Try Clustal Omega.

[sunnykevin97]

Well, my analysis focuses on aDNA genome analysis. Reconstruction of phylogeny based on the dN/dS (Non non synonymous/synonymous),by comparing different elephant genomes. To proceed further, for positive selection analysis the tool needs MAF (Multiple alignment file) format as an input. Could you list out some alignment tools, which generates MSA alignment output into MAF (Multiple alignment format). that would be nice. thanks!