Bug#409640: ITP: mafft -- Multiple alignment program for amino acid or nucleotide sequences

[Charles Plessy <charles-debian-nospam@plessy.org>]

Le Sun, Feb 04, 2007 at 11:05:08AM -0600, Ron Johnson a écrit :
> On 02/04/07 08:27, Charles Plessy wrote:
> > 
> > MAFFT is a multiple sequence alignment program for unix-like operating
> > systems.  It offers a range of multiple alignment methods, L-INS-i
> > (accurate; recommended for <200 sequences), FFT-NS-2 (fast; recommended
> > for >2,000 sequences), etc.
> 
> What do you use for nucleotides between 200 and 2000 sequences?

Hi,

thanks for the input. Here is a revised description:

 MAFFT is a multiple sequence alignment program, which offers three
 accuracy-oriented methods:
  * L-INS-i (probably most accurate; recommended for <200 sequences;
    iterative refinement method incorporating local pairwise alignment
    information),
  * G-INS-i (suitable for sequences of similar lengths; recommended for
    <200 sequences; iterative refinement method incorporating global
    pairwise alignment information),
  * E-INS-i (suitable for sequences containing large unalignable regions;
   recommended for <200 sequences),
 and five speed-oriented methods:
  * FFT-NS-i (iterative refinement method; two cycles only),
  * FFT-NS-i (iterative refinement method; max. 1000 iterations),
  * FFT-NS-2 (fast; progressive method),
  * FFT-NS-1 (very fast; recommended for >2000 sequences; progressive
    method with a rough guide tree),
  * NW-NS-PartTree-1 (recommended for ∼50,000 sequences; progressive
    method with the PartTree algorithm).