The ability to do gene homology alignments was added in Lasergene 17.6, released in early 2024. This method is for nucleotide sequences only and is set up using a simple wizard with five screens. With this method, you can perform a phylogenetic analysis of much larger sequences than those supported by most multiple sequence alignment algorithms.
A gene homology alignment aligns an entire genome from scratch; a feature that is shared by the Mauve method. By contrast, the other alignment algorithms used in MegAlign Pro are considered single block alignment methods.
MegAlign Pro starts by identifying a subset of homologous genes in bacterial genomes or eukaryotic chromosomes. It then creates a concatenated protein from each genome and aligns these against a reference sequence using the MAFFT algorithm. The results can be viewed in the Homologs view, and a phylogenetic tree can be created, if desired. When generating a tree, we recommend using the RaXML-NG algorithm due to its speed and expanded capacity.
To launch the gene homology alignment wizard:
Do either of the following:
- From the Welcome screen’s New Project tab, choose Align by gene homology.
- From any location, choose the menu command Align > Align by Gene Homology.
In both cases, a wizard opens that is similar to the one used in DNASTAR’s SeqMan NGen application. Each wizard screen is described in a separate topic:
The alignment progress is shown in a progress bar and can also be observed in the Console panel. Once the alignment is complete, see Analyzing a gene homology alignment to learn the next steps.
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