MAFFT (Multiple Alignment using Fast Fourier Transform) is a fast multiple alignment program suitable for large alignments. To use MAFFT, you must first download the plugin by going to Plugins under the Tools menu and selecting MAFFT Multiple Alignmen from the list of available plugins. Click the Install button to install it, and then click OK to close the Plugins window. To run MAFFT, select the sequences or alignment you wish to align, select the Align/Assemble button from the Toolbar and choose Multiple Alignment. MAFFT should now be showing as an option for the type of alignment.
For more information on MAFFT and its options, please refer to the original documentation for the program: http://mafft.cbrc.jp/alignment/software/.
The Mauve aligner allows you to construct whole genome multiple alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. To use Mauve, you must first download the plugin by going to Plugins under the Tools menu and selecting Mauve from the list of available plugins. Click the Install button to install it, and then click OK to close the Plugins window. To run Mauve, select the sequences or alignment you wish to align, select the Align/Assemble button from the Toolbar and choose Align Whole Genomes.
An alignment produced by Mauve is displayed in the Mauve genome alignment viewer, which allows you to easy see aligned blocks of sequence and genome rearrangements. Note that this is not a regular Geneious alignment document and you cannot run downstream analyses such as tree building from this document. To run downstream analyses you must first extract the local alignment blocks. To do this, switch to the Alignment View tab above the sequence viewer and if you have more than one local alignment block, choose which one you wish to extract in the General tab to the right of the sequence viewer. Then select all the sequences in that alignment and click Extract. Choose the option to extract the sequences as an alignment, and a separate alignment document will be created in the document table.
For more information on Mauve and its options, please refer to the original documentation for the program: http://darlinglab.org/mauve/mauve.html.
LASTZ is designed for pairwise alignments of whole genomes and can efficiently align chromosomal or genomic sequences millions of nucleotides in length. To use LASTZ, you must first download the plugin by going to Plugins under the Tools menu and selecting LASTZ from the list of available plugins. Click the Install button to install it, and then click OK to close the Plugins window. To run LASTZ, select the sequences or alignment you wish to align, select the Align/Assemble button from the Toolbar and choose Align Whole Genomes.
For more information on LASTZ and its options, please refer to the original documentation for the program: http://www.bx.psu.edu/~rsharris/lastz/