MUSCLE
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MUSCLE(multiple sequence comparison by log-expectation) is a public domain, multiple sequence alignment software for protein and nucleotide sequences. MUSCLE is often used as a replacement for Clustal, since it typically (but not always) gives better sequence alignments; in addition, MUSCLE is significantly faster than Clustal, especially for larger alignments (Edgar 2004). MUSCLE is split in three phases : i) k-mer counting to judge similarity and preliminary tree building ii) improve the results by iteratively constructing progressive alignments using the most recent tree generated iii) iterative refinement by removing superfluous Indels (Wikipedia\, Edwards 2009)