Best paper award
MUSCLE awarded "ISMB/ECCB Best Paper Award" at ISMB 2004.
MUSCLE 3.41
New features and fixes:
- CLUSTALW output format
- HTML output format with conservation coloring
- N-terminal methionines align neutrally (avoids artifacts)
- Similar sequences grouped together (makes visual inspection easier)
- New -stable option to preserve input order of sequences (grouping did not work correctly in 3.4)
- New -version option to report current version
- Bug fix: memory usage on Linux now displayed correctly
- Bug fix: "too many open files" problem fixed (bug in 3.4 only)
MUSCLE 3.52
New features and fixes:
- MSF output format improved GCG compatibility (thanks to Eric Martel for help on this one)
- User-defined guide tree (-usetree option added)
- Maximum memory limit to prevent paging (-maxmb option added)
- Bug fix: "DiagList::Add, overflow" error.
MUSCLE v6 withdrawn
We have withdrawn MUSCLE v6. We found that the improvement in speed and memory use compared with PROBCONS did not justify maintenance of a second program. We recommend PROBCONS for highest accuracy for smaller numbers of sequences, and MUSCLE for high-throughput applications and larger numbers of sequences.
PREFAB v4 now available
A new version of PREFAB is available. See here for download. This version cleans up several issues and adds a new reference set with over-represented subfamilies.