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). . Homepage: http://align.bmr.kyushu-u.ac.jp/mafft/software/ Have a nice day, -- Charles Plessy http://charles.plessy.org Wako, Saitama, Japan -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]