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MUSCLE documentation
  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

  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


  Technical support
  "MSA::GetLetter" bug
  -stable option bug
  "Matrix is not symmetrical" warning
  Very large alignments are usually a bad idea
  Phylogenetic trees are not good guide trees
  Problems with BALIBASE