Mauve alignment options

The Mauve alignment algorithm is for genome level alignment of nucleotide sequences. To run a Mauve alignment, select two or more nucleotide sequences and choose Align > (Re)Align Using Mauve.

If you wish to change method options, instead choose Align > Align with Options.

Change settings as desired:

• Use the Align drop-down menu to select sequences to align or realign.

• In the Using drop-down menu, choose Mauve.

• If the Default seed weight box is checked, as it is by default, the optimal seed weight (number of matches required per k-tuple) is calculated automatically. You may uncheck the box and either use the slider or manually enter a number in the Seed weight box to specify a particular seed weight between 3 and 21. The default is 15.

• Check the Use seed families box to use multiple spaced seed patterns to identify potential homology. When working with divergent genomes, checking this box can significantly improve the sensitivity and accuracy of the alignment.

• Whether or not you have checked either of the boxes in this dialog, you may override the default Min LCB weight, if desired, by entering a value in the box. Increasing the Min LCB weight may reduce the number of spurious rearrangements, and is advisable in many cases.

The following table shows how the MegAlign Pro settings correspond with settings in Mauve online.

After making your changes:

• Choose Align to use the entered options to perform a multiple sequence alignment.

• Use the Reset to Default button if you would like to reset all values to the MegAlign Pro defaults.

• Select Cancel to leave the dialog without saving any changes.

The following videos demonstrate how to perform a multiple alignment using the Mauve alignment algorithm:

The following video shows a multiple alignment using the Mauve algorithm: