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Alignment

Multiple Sequence Alignment
Align sequences given in a multi-fasta file

Before constructing phylogenetic (evolutionary) trees, sequences need to re-arranged to match best to each other, for example, by inserting gaps. There exits several tools for sequence alignment including MAFFT and MUSCLE.
If you have more than 200 sequences, try → PASTA or → UPP. If your sequences are fragmented, try → UPP. 

For short read alignment, see → bowtie2 or  → BWA

MAFFT

Download and Install
sudo apt-get update
sudo apt-get install mafft
Run mafft
mafft --localpair --maxiterate 1000  sequences.fasta > aligned_sequences.aln
http://mafft.cbrc.jp/alignment/software/algorithms/algorithms.html

  --maxiterate 1000  for less than 200 sequences
  --globalpair (instaed of --localpair)  for sequences of similar lengths


MAFFT online web-tool
http://mafft.cbrc.jp/alignment/server/

MUSCLE

MUltiple Sequence Comparison by Log-Expectation
http://www.drive5.com/muscle/

Download and install on Ubuntu
wget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
tar -zxvf muscle3.8.31_i86linux64.tar.gz
mv muscle3.8.31_i86linux64 muscle
mv muscle tools/   # move to your tools/ directory
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/

Clustal Omega

protein sequence alignment tool
sudo apt-get update
sudo apt-get install clustalo


Example (command line)
clustalo -i sequences.fasta -o aligned_sequences.fasta --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




Subpages (1): Alignment viewer