Please note that we will be retiring this old site on Tuesday, August 25th, 2015.
At that point, the URL for will bring you to our new site currently hosted at We encourage you to visit the new site now and see a more recent set of updated gene annotations and MANY more Pseudomonas strains.
Pseudomonas Genome Database - Mauve Alignment Viewer

View Pre-computed Pseudomonas Genome Alignments With Mauve


The ability to perform whole-genome alignments of Pseudomonas species' genomes is essential for identifying large-scale evolutionary events including inversions, rearrangements and horizontal transfer that have taken place, such as the insertion of genomic islands. The Pseudomonas Genome Database facilitates this by incorporating pre-computed, whole-genome alignments based on the Mauve software package (Darling et al., 2004). For strains of the same species, genomic DNA sequences of the largest chromosomes were aligned using the Progressive Mauve algorithm.

We have made the mauve alignments available for download and viewing on your PC or Mac.


  • Download and install Mauve.
  • Download one of the .zip files below. Each .zip contains the pre-computed alignment and Genbank files containing annotations for each sequence. You will need a program such as WinRAR to open these files.
  • Open mauve. Under File, select the Open alignment... option.
  • Navigate to the directory containing the files that were just unzipped. Choose a file resembling P_aeruginosa_progressive_mauve that does NOT have a file extension.


  • Pseudomonas aeruginosa - Alignment of strains PAO1, PA14, LESB58, PA7, 2192, 39016, C3719 and PACS2 (file:, 234MB).
  • Pseudomonas syringae - Alignment of strains DC3000, B728a and 1448A (file:, 82MB).
  • Pseudomonas fluorescens - Alignment of strains Pf-5 , Pf0-1 and SBW25 (file:, 90MB).
  • Pseudomonas putida - Alignment of strains F1 , GB-1, KT2440 and W619 (file:, 107MB).