Phineus provides a one stop solution for the processing of ABI chromatograms for MLST and MLSA projects, where each consensus sequence for each locus is generated by assembling 8 or less reads..

• Phineus 1.0 comes preinstalled with settings for processing chromatograms for use in MLST projects defined at http://www.mlst.net

• Chromatogram importing
  • Chromatograms can be imported from networked drives, or local fixed and removable disks.
  • multiple plates can be imported at the same time.
  • Phineus is able to import data from multiple plates (made up of either 96 or 384 wells) using a comma separated file format
• Chromatogram processing
  The basecaller Phred is utilised and a quality clipping moduleis incorporated which makes use of Phred quality scores
  • A trimming module, can be used to enable the generation of a consensus sequence of known size (with known start and/or end points) or of unknown size (but bounded by a known start and a known end sequence)
• Editing
  • Allows automatic reverse complementing reverse direction traces, to ensure that both traces are comparable
  • "snap-to-view" of traces to positions as they are selected in the alignment view
  • For MLST projects, the retreival and assignation of allele numbers and sequence types is achieved automatically from http://www.mlst.net
• Data Storage
  • Phineus provides backup and restore capabilities for your data
  • Phineus provides an interface for reviewing data as you produce it, in the context of the rest of the data you have generated
  • Phineus provides a mechanism for the bulk submission both of strains of known sequence type, and also for strains containing unknown alleles and unkown sequence types
  • By making use of the industry leading database Postgres, Phineus is able to securely store your data.
• Other features
• eBURST analysis can be undertakento facilitate comparisons within the locally stored and generated dataset, and between local data and the MLST website.
• Data can be exported in several file formats (csv, FASTA) for use with other software packages

Known Bugs

None reported. We encourage feedback and error / BUG reporting, should you have any queries, bug reports or questions please contact Tom Connor or David Aanensen

Phineus has been developed by Tom Connor and is hosted at
The Department of Infectious Disease Epidemiology
Imperial College London
Funded by the Wellcome Trust