Question: Multiple whole genome alignment
gravatar for robjohn7000
2.8 years ago by
United Kingdom
robjohn700070 wrote:


Does anyone know of any whole genome alignment tool that can handle 200-300 bacteria genome?


ADD COMMENTlink modified 2.7 years ago by Chrispin Chaguza220 • written 2.8 years ago by robjohn700070

Along with the suggestions below, you can also consider SyMap which used Mummer and Promer for genome alignment.

ADD REPLYlink written 2.7 years ago by geek_y8.3k
gravatar for HG
2.8 years ago by
HG1.0k wrote:

Please have a look 


ADD COMMENTlink written 2.8 years ago by HG1.0k

+1 for Mauve. It is now located at: You will need access to a machine with plenty of RAM for working with 200+ genomes.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by genomax44k

Yes, its need plenty of ram according to your data set. But for such a huge data set core genome alignment will be always better than whole genome alignment. Such as HarvestTools could be better choice.

ADD REPLYlink written 2.8 years ago by HG1.0k

Thanks guys. I really appreciate your suggestions and useful information.

ADD REPLYlink written 2.8 years ago by robjohn7000090
gravatar for Chrispin Chaguza
2.7 years ago by
University of Liverpool, UK
Chrispin Chaguza220 wrote:

For that many bacterial genomes, whole genome alignment would either be impractical or might take very long time and require lots of computational resources to properly align them especially if working with a species that has high rates of genetic recombination/horizontal gene transfer such as Streptococcus pneumoniae. In such species, most people usually work with a core genome alignment (merged alignment of all the genes present in a species/dataset) for phylogenetic analysis etc. This approach would not be appropriate if you're particularly interested in non-coding regions for example, rearrangements etc.

Tools that you could use are; GET_HOMOLOGUES (, ROARY (, CD-HIT (

ADD COMMENTlink modified 2.6 years ago • written 2.7 years ago by Chrispin Chaguza220

Many thanks for further useful information @Chrispin.Much appreciated!

ADD REPLYlink written 2.6 years ago by robjohn7000090
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