Multiple sequence alignment

Progressive alignment first builds a guide tree from k-mer distances, then aligns sequences and groups from the closest to the most distant along the tree; it suits up to a few dozen homologous sequences of up to a few thousand residues.

In the coloured view identical or similar residues share a colour, and the conservation bar below is taller for more uniform columns; scroll sideways to see the full length.

Conservation marks in the Clustal text: “*” all identical, “:” a strongly similar group of amino acids, “.” a weakly similar group, space not conserved or gapped.

Alignment quality depends on similarity: below about 25% identity, protein alignments become much less reliable. To build a tree, pass the FASTA result to the neighbour-joining tree tool.

Method

Progressive alignment: Feng & Doolittle 1987 (J Mol Evol 25:351); k-mer distance: Edgar 2004 (Nucleic Acids Res 32:1792); conservation groups as in Clustal (Thompson et al. 1994, Nucleic Acids Res 22:4673).

Data size

Up to 50 sequences of up to 2,000 nt/aa each; for larger alignments, see “Need a full analysis?” at the bottom of this page.