MUSCLE

	Getting started Installing MUSCLE Making an alignment (MSA) Creating a tree (N-J or UPGMA) License: MUSCLE is public domain MUSCLE papers, how to cite Papers and citing MUSCLE Popular options and features Alignment output formats Adding a sequence to an existing MSA Profile-profile alignment (aligning two MSAs) Refining (improving) an existing MSA Options For highest accuracy For large datasets For fastest speed Command line reference	Advanced features (rarely used) Guide tree output files Using a pre-computed tree Using a custom substitution matrix Distance options Clustering (tree-building) options Diagonals Anchors Support Technical support "MSA::GetLetter" bug -stable option bug "Matrix is not symmetrical" warning Discussions Very large alignments are usually a bad idea Phylogenetic trees are not good guide trees Problems with BALIBASE