Align large genomes using LASTZ

LASTZ Plugin

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.

Quick Start

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.


7.0.3 (14 Jul 2022) – Download for Geneious 2020.0

– Updated LastZ to version 1.04.15

7.0.2 (06 Mar 2019) – Download for Geneious 8

– Fixed occasional crash in progress dialog trying to display a warning

7.0.1 (15 Nov 2016) – Download for Geneious 7.0

– 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.


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