Without the -6merpair flag, too slow for this purpose.Ī similar option, -add, is not efficient for this purpose, but suitable when the input sequences are less closely related, the sequences to be added are fewer and a reference MSA is available. % mafft -6merpair -thread -1 -keeplength -addfragments othersequences referencesequence > output Which removes sequences that have more than 5% ambiguous letters. % mafft -6merpair -maxambiguous 0.05 -addfragments othersequences referencesequence > output If the input data contains many ambiguous letters, try: % mafft -6merpair -keeplength -addfragments othersequences referencesequence > output If selecting the " Keep alignment length" option below in the input page, no gaps are inserted to the reference sequence, ie, corresponding sites in the other sequences are deleted.Īs a result, the numbering of sites is kept and the calculation is faster than the default in some cases.ĭon't change the " Strategy" switch from Auto when the sequences are long.įor less closely related sequences (% identity output The page title, addfragments, and labels of the two input boxes are not directly descriptive for this usage,īecause this function is originally for another purpose. Select options ( Adjust direction, Keep alignment length, etc) as necessary. Input the other sequences to the " New sequence(s)" box. Input the reference (eg, NC_045512.2) to the " Reference" box. Select a single reference sequence or a reference MSA (a small set of sequences already aligned). Reduced the frequency of "timeout" error in data transfer, 2020/Jul/27.Įarlier versions (≤7.458) had the same options but were inefficient for this purpose. Online version supports more than 20,000 sequences × ∼30,000 sites, 2021/Jan. Time complexity is O( N L log L), where N is the number of sequences and L is sequence length. The scale factor used to calculate the score is provided by the scoring matrix. When the input data set is large and the sequences are very closely related (% identity ∼ 99), it's sometimes useful to align all sequences just to a reference to build a full MSA. Score swalign(Seq1, Seq2) returns the optimal local alignment score in bits. Rapid calculation of full-length MSA of closely-related viral genomes Experimental (2020/Apr/11 )
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