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Associated diseases

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TreeKO specifications

Information


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

Subtool


  • ETE

Versioning


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Maintainer


  • person_outline Toni Gabaldón <>

Publication for TreeKO

TreeKO in publications

 (2)
PMCID: 3616871
PMID: 23432914
DOI: 10.1186/1471-2164-14-123

[…] 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 ). […]

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 […]


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

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