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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
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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
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