mafft-homologs1

The accuracy of an alignment of a few distantly related sequences is considerably improved when being aligned together with their close homologs. The reason for the improvement is probably the same as that for PSI-BLAST. That is, the positions of highly conserved residues, those with many gaps and other additional information is brought by close homologs. According to Katoh et al. (2005), the improvement by adding close homologs is 10% or so, which is comparable to the improvement by incorporating structural information of a pair of sequences. Mafft-homologs in a mafft server works like this:

-a n

The number of collected sequences (default: 50).

-e n

Threshold value (default: 1e-10).

-o xxx

Options for mafft (default: " --op 1.53 --ep 0.123 --maxiterate 1000 --localpair --reorder").

-l

Locally carries out BLAST searches instead of NCBI BLAST (requires locally installed BLAST and a database).

-f

Outputs collected homologues also (default: off).

-w

entire sequences are subjected to BLAST search (default: well-aligned region only)

MAFFT version > 5.58.

Either of

Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment.