MLOGD: Supplementary material

• Some additional information for Firth AE, Brown CM (2006) Detecting overlapping coding sequences in virus genomes. BMC Bioinformatics 7:75 - details on some sensitivity and selectivity tests using real sequence data (virus alignments): pdf file (0.3MB, 8 pages, 5 figures).
  
  
• Note on how to include your own amino acid, codon and nucleotide mutation matrices, instead of the default ones, if you are using the downloadable programmes.
  
  
• List of some minor changes to the algorithms since Firth & Brown, 2005, Bioinformatics, 21, 282-92.
  
  
• Extract from Firth & Brown, 2005, Bioinformatics, 21, 282-92, Supplementary Material. Covers read-frame notation; sequence evolution model; MLOGD, N123 and NsNn statistics and classification; sensitivity of classification as a function of sequence length; sensitivity to sequencing errors and to choice of mutation matrices; and triple coding. pdf file (1.0MB), ps file (0.9MB).
  
  
• Tests on overlapping genes in E. coli and S. typhimurium genomes: pdf file (1.2MB), ps file (0.8MB).