Align-m - multiple alignment

Align-m v2.3 is currently available as a binary for Linux/x86 and Windows/x86.

Click here to download it, or just view the manual.
Questions, remarks or problems can be sent to

Align-m is an accurate and highly versatile multiple alignment program. It consists of 3 modules, S2P, P2P and P2M (see figure, manual), which can be used separately or consecutively to accomplish several tasks:
- Multiple sequence alignment
- Include extra information to guide the sequence alignment
- Multiple structure alignment
- Homology modeling by (iteratively) combining sequence and structure alignment data
- 'Filtering' of Blast or other pairwise alignments
- Combining many alignments into 1 consensus
- Multiple genome alignment (can cope with rearrangements)

The drawback is that it does not run fast: 20 sequences of length 250 will generally require a few minutes to pass through all 3 modules. Above 50 sequences, this will require in the order of hours. For specific problems however, the running time is usually not so important.

Code history:
2005/01/06 v2.3 added option to improve alignment of sequences with clear subsets, such as for mapping a number of homologous sequences onto a multiple structure alignment, based on a few anchor points
2004/11/25 v2.2 added possibility for a much faster and less memory intensive 'unguided' mode of the S2P module, which is generally less accurate in terms of correct residue pairs that it finds back, but which also aligns a very low fraction of residues incorrectly; added '-s2p_minscore' option for a more flexible tuning of the 'guided' mode
2004/10/17 v2.1 added built-in support for DNA and RNA sequences; linux version compiled to statically linked executable to avoid problems with different distributions.
2004/08/24 v2.1 released. S2P can now accept alignment constraints as well.
2004/07/13 v2.0 released. P2M module added, which produces a true multiple lignment. A few bugs in S2P and P2P fixed.
2003/07/31 v1.0 released. S2P and P2P produce a set of pairwise alignments, or a multiple alignment by aligning these to a reference.

Figure: Align-m data flow

Scoring alignments

Part of the SABmark database is the program score_alignments that will score an alignment given a reference alignment, in terms of the number of residues aligned correctly and incorrectly. Both reference and test alignments may be pairwise or multiple alignments, and the test alignments may contain multiple solutions. It accepts the Fasta, Clustal and Alignm formats. Download it here, or view the SABmark manual for further specifications.