Rapid calculation of full-length MSA of closely-related viral genomes Experimental (2020/Apr/11 )
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.
Time complexity is O
), where N
is the number of sequences and L
is sequence length.
Online version supports more than 20,000 sequences × ∼30,000 sites, 2021/Jan.
Online version supports up to ∼ 20,000 sequences × ∼30,000 sites, 2020/Apr/18.
Reduced the frequency of "timeout" error in data transfer, 2020/Jul/27.
On command line, use
version 7.467 or later.
Earlier versions (≤7.458) had the same options but were inefficient for this purpose.
Input page Updated 2022/Mar
Select a single reference sequence or a reference MSA (a small set of sequences already aligned).
Input the reference (eg, NC_045512.2) to the "Reference" box.
Input the other sequences to the "New sequence(s)" box.
Select options (Adjust direction, Keep alignment length, etc) as necessary.
The page title, addfragments, and labels of the two input boxes are not directly descriptive for this usage,
because this function is originally for another purpose.
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.
As a result, the numbering of sites is kept and the calculation is faster than the default in some cases.
Don't change the "Strategy" switch from Auto when the sequences are long.
For less closely related sequences (% identity < ??), normal MSA calculation is probably necessary.
A similar option, addsequences, 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.
Command Updated 2021/Jan/29
After dividing the input sequences into reference and others,
% mafft --6merpair --addfragments othersequences referencesequence > output
To keep the numbering of sites,
% mafft --6merpair --keeplength --addfragments othersequences referencesequence > output
(sometimes faster than the default).
If the input data contains many ambiguous letters, try:
% mafft --6merpair --maxambiguous 0.05 --addfragments othersequences referencesequence > output
which removes sequences that have more than 5% ambiguous letters.
Available in versions ≥7.473.
Runs efficiently in parallel,
% mafft --6merpair --thread -1 --keeplength --addfragments othersequences referencesequence > output
Without the --6merpair flag, too slow for this purpose.
A 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.