(Mock-up of) Administrator query:

Construct a phylogenetic distance matrix

We use a page like this to construct our distance matrices.
If you would like a custom distance matrix constructed for yourself, please send us a request by email specifying the parameters that interest you. You must, however, be a registered user in order to take advantage of this service.
Download our ready-made trees (for methods, see Gophna et al. 2005. J. Bacteriol. 187, 1305-1316); you will need a program such as TreeViewX in order to display the trees:

222-taxon unweighted tree
222-taxon concordance-weighted tree
222-taxon discordance-weighted tree (see Gophna et al. for interpretation)
229-taxon unweighted tree

more information...

Choose a BLASTP cutoff e-value (1.0e-300 to 1.0e-3): 1.0e-

Select the matrix type:
(Clarke, G.D.P., R.G. Beiko, M.A. Ragan & R.L. Charlebois. 2002. Inferring genome trees using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J. Bacteriol. 184, 2072-2080.)

Based on normalized BLASTP, including PDS genes
Based on normalized BLASTP, excluding PDS genes
Based on shared proportions of genes

Select functional categories by entering a string of codes, if desired:
(Charlebois, R.L., R.G. Beiko & M.A. Ragan. 2004. Genome phylogenies. In: (R.P. Hirt & D.S. Horner, eds.) Organelles, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics, CRC Press, Boca Raton FL, pp. 189-206.)

The remaining options are applicable only to matrices computed using normalized BLASTP scores:

Select the number of bootstraps:

No bootstrapping
10 bootstraps
20 bootstraps
50 bootstraps
100 bootstraps

Select the jackknifing proportion:

No jackknifing
Jackknifing proportion of 25 percent
Jackknifing proportion of 50 percent
Jackknifing proportion of 75 percent

Select a weighting model:
(Gophna, U., W.F. Doolittle & R.L. Charlebois. 2005. Weighted genome trees: refinements and applications. J. Bacteriol. 187, 1305-1316.)

Unweighted
Weighted for concordance
Weighted for concordance squared
Weighted for discordance
Weighted for discordance squared
Weighted for prevalence
Weighted for rarity
Weighted for concordance and prevalence
Weighted for discordance and rarity