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. 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 lengthsMAFFT online web-tool http://mafft.cbrc.jp/alignment/server/ MUSCLEMUltiple Sequence Comparison by Log-Expectationhttp://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/ directoryhttp://www.drive5.com/muscle/downloads.htm Run muscle
muscle -in sequences.fasta -out aligned_sequences.aln http://www.ebi.ac.uk/Tools/msa/muscle/ sudo apt-get update 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 |
Tools > Phylogenetic tree >
Sequence-Alignment
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Alignment viewer