Multiple Sequence Alignment
Alignment of sequences means to re-arrange original sequences such that the location of similar bases match best to each other (by adding space / inserting gaps).
Aligned sequences are required, for example, for constructing phylogenetic (evolutionary) trees.
There exits several tools for sequence alignment including MAFFT and MUSCLE. Original sequences have to be provided as → multi-fasta file with all sequences in identical direction (corrected for forward and reverse strand).
For short read alignment (shotgun sequencing), see → bowtie2 or → BWA
Check final alignment results, using → Alignment viewer
Download and Install
sudo apt-get update
sudo apt-get install mafft
http://mafft.cbrc.jp/alignment/software/
Run MAFFT to align different variants of a DNA (gene) sequence
mafft --localpair --adjustdirectionaccurately --maxiterate 1000 sequences.fasta > aligned_sequences.aln
--adjustdirectionaccurately to correct sequence direction (forward or reverse)
--maxiterate 1000 for less than 200 sequences
--globalpair (instaed of --localpair) for sequences of similar lengths
https://mafft.cbrc.jp/alignment/software/algorithms/algorithms.html
https://mafft.cbrc.jp/alignment/software/adjustdirection.html
MAFFT online web-tool
http://mafft.cbrc.jp/alignment/server/
MUltiple Sequence Comparison by Log-Expectation
Download and install on Ubuntu
sudo apt install muscle
http://www.drive5.com/muscle/downloads.htm
Run muscle
muscle -in sequences.fasta -out aligned_sequences.aln
Muscle online web-tool
http://www.ebi.ac.uk/Tools/msa/muscle/
protein sequence alignment tool
Install on Ubuntu
sudo apt-get update
sudo apt-get install clustalo
Example (command line)
clustalo -i sequences.fasta -o aligned_sequences.aln --auto -v
--auto set alignment options automatically
-v print "verbose" progress info
# see more options
clustalo --help
Clustal Omega online web-tool
http://www.ebi.ac.uk/Tools/msa/clustalo/ (max 4000 sequences)
http://www.genome.jp/tools/clustalw/
Documentation
http://www.clustal.org/omega/README
See also: