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TreeKO specifications


Unique identifier OMICS_11552
Name TreeKO
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The input of treeKO are two bifurcated phylogenetic trees in which the species source for the different sequences is indicated (by default a three letters pre-fix is expected). The entry trees should be rooted or a rooting strategy indicated (midpoint rooting is used by default if an un-rooted tree is provided; an option to minimize the total number of inferred duplication is also implemented).
Input format Newick
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes


  • ETE


No version available


  • person_outline Toni Gabaldón

Publication for TreeKO

TreeKO citations


ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

Mol Biol Evol
PMCID: 4868116
PMID: 26921390
DOI: 10.1093/molbev/msw046

[…] ETE v3 provides three measures to compute distances between trees, namely the Robinson–Foulds distance (), a branch congruence measure (%) and the TreeKO Speciation distance (). In contrast to existing software (; ), ete-compare calculates all three distances at the same time; it accepts trees varying in size and containing duplication events; i […]


Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

Mol Biol Evol
PMCID: 4209138
PMID: 25158799
DOI: 10.1093/molbev/msu245

[…] rd method looks for clusters with monophyletic outgroups (MO), roots the tree, and infers gene duplication in a similar way as RT. Both RT and MO are similar to the tree-pruning method implemented in TreeKO () in that both traverse a rooted tree from root to tips and prune at nodes with taxon duplications. The two differ in that TreeKO considers all possible decompositions, calculates the pairwise […]


Comparative transcriptomics of early dipteran development

BMC Genomics
PMCID: 3616871
PMID: 23432914
DOI: 10.1186/1471-2164-14-123

[…] on of 16,894 gene-trees (provided in Additional file ) that resulted from the combination of the four generated phylomes (see above) were used to infer several supertree-based phylogenies. First, the TreeKO algorithm [], and the ETE toolkit [] were used to construct a list of 32,437 species-tree topologies represented in all gene evolutionary histories (provided in Additional file ). This methodol […]


Deciphering a global network of functionally associated post translational modifications

Mol Syst Biol
PMCID: 3421446
PMID: 22806145
DOI: 10.1038/msb.2012.31

[…] v2.0 was used to map every protein in the data set to the oldest eukaryotic OG in which the protein is present and generated a multiple sequence alignment (MSA) and sequence tree using PhyML v.3.30. TreeKO () algorithm was used to root the tree and decompose the sequence tree into a set of all possible pruned trees with no duplications and in consonance with the species tree topology. The set of […]

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TreeKO institution(s)
Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain

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