Align large genomes using LASTZ
Requires Geneious 7.0+
LASTZ (Large-Scale Genome Alignment Tool) is a fast and powerful alignment tool for the pairwise alignment of genomic DNA sequence. LASTZ was designed with large-scale genomic analysis in mind and can efficiently align chromosomal or genomic sequences millions of nucleotides in length. It identifies orthologous regions between genomic sequences on a massive scale using a methodology that ignores the coding-region bias.
Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).
Once installed, run the plugin by selecting two or more nucleotide sequences and clicking on Align/Assemble - Align Whole Genomes in the toolbar. LASTZ is available as an option at the top of the Alignment options window.
The results are presented as a collection of multiple alignments, one for each reference sequence with orthologous regions from the other sequences aligned to them. A dotplot is also displayed inside the Alignment view.
7.0.1 (15 Nov 2016)
- Automatically select the result if there is a single result
- Fix crash when fragment of reference sequence in axt file begins with a gap
Harris, R.S. (2007) Improved pairwise alignment of genomic DNA. Ph.D. Thesis, The Pennsylvania State University.