help

MAFFT

user: GUEST

Sequence Input Paste your sequences in this text area (supported formats) examples FASTA format identifiers
Limitations:	Maximum number of sequences is 300 Maximum total length of sequences is 150000
References:	K. Katoh, K. Kuma, H. Toh and T. Miyata MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005 Jan; 33:511-518. K. Katoh, K. Misawa, K. Kuma and T. Miyata MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002 Jul; 30:3059-3066.

Parameters
Matrix	BLOSUM30 BLOSUM45 BLOSUM62 (default) BLOSUM80 PAM120 PAM250
Opening gap penalty
Extending gap penalty/Offset value
Strategy	FFT-NS-1: Very rough & very fast (>2000 sequences); progressive method FFT-NS-2: Rough & fast; progressive method FFT-NS-i-2: Medium; iterative refinement method, two cycles only FFT-NS-i: Accurate and slow; iterative refinement method G-INS-i: Suitable for global alignment L-INS-i: Most accurate in many cases, for a single domain E-INS-i: Accurate for multiple domains

MyHits © 2003-2009