Phylogenetic Reconstruction from Non-Genomic Data

Copyright © 2006 J. C. Clemente, K. Satou, G. Valiente


The Phylogenetic Reconstruction from Non-Genomic Data tool allows you to cluster a set of organisms based on their metabolic pathways. You have a choice of selected organisms and metabolic pathways taken from KEGG, three enzyme similarity measures (gene ontology, hierarchical, information content), two clustering methods (UPGMA or neighbor-joining), the choice of full names or KEGG abbreviations, and the value of the α parameter (relative weight of compounds and enzymes in assessing the similarity of enzymatic reactions).

The output is a reconstructed phylogenetic tree for the selected set of organisms, both in Newick format and as a cladogram

[changes]

Select set of organisms

KEGG Animals Vertebrates Mammals Homo sapiens hsa
Mus musculus mmu
Rattus norvegicus rno
Insects Drosophila melanogaster dme
Anopheles gambiae (Draft) daga
Nematodes Caenorhabditis elegans cel
Bacteria Proteobacteria Gamma/Enterobacteria Escherichia coli K-12 MG1655 eco
Gamma/Others Haemophilus influenzae hin
Beta Neisseria meningitidis MC58 (serogroup B) nme
Firmicutes Bacillales Listeria innocua lin
Clostridia Clostridium perfringens cpe
Archaea Euryarchaeota Methanococcus jannaschii mja
Archaeoglobus fulgidus afu

Select set of metabolic pathways

Metabolism Carbohydrate Metabolism Glycolysis / Gluconeogenesis 00010
Citrate cycle (TCA cycle) 00020
Pentose phosphate pathway 00030
Pentose and glucuronate interconversions 00040
Fructose and mannose metabolism 00051
Galactose metabolism 00052
Ascorbate and aldarate metabolism 00053
Pyruvate metabolism 00620
Glyoxylate and dicarboxylate metabolism 00630
Propanoate metabolism 00640
Energy Metabolism Oxidative phosphorylation 00190
Lipid Metabolism Fatty acid biosynthesis 00061
Fatty acid metabolism 00071
Biosynthesis of steroids 00100
Nucleotide Metabolism Purine metabolism 00230
Pyrimidine metabolism 00240
Amino Acid Metabolism Glutamate metabolism 00251
Alanine and aspartate metabolism 00252
Glycine, serine and threonine metabolism 00260
Methionine metabolism 00271
Cysteine metabolism 00272
Valine, leucine and isoleucine degradation 00280
Valine, leucine and isoleucine biosynthesis 00290
Lysine degradation 00310
Urea cycle and metabolism of amino groups 00220

Enzyme similarity measure

Clustering method

Organisms full name in output

Alpha value [0-1]

Similarity matrices (debug only)