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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

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
 
Discussions
  Very large alignments are usually a bad idea
  Phylogenetic trees are not good guide trees
  Problems with BALIBASE
 
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