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