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CITUP specifications


Unique identifier OMICS_07438
Alternative name Clonality Inference in Tumors Using Phylogeny
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline S. Cenk Sahilp

Publication for Clonality Inference in Tumors Using Phylogeny

CITUP citations


Genetic Evidence for Early Peritoneal Spreading in Pelvic High Grade Serous Cancer

PMCID: 5858520
PMID: 29594039
DOI: 10.3389/fonc.2018.00058

[…] Variant allele frequencies for filtered somatic non-synonymous SNVs from three callers were used for phylogenetic tree analysis using the CITUP bioinformatics tool (). Iterative method called CITUP_iter, included in the CITUP program, was used to generate trees with up to nine nodes. The optimal trees and proportional representation of […]


Computational Methods for Characterizing Cancer Mutational Heterogeneity

Front Genet
PMCID: 5469877
PMID: 28659971
DOI: 10.3389/fgene.2017.00083

[…] bution over possible evolutionary trees. PhyloWGS (Deshwar et al., ) builds on PhyloSub and allows the reconstruction of tumor evolution from SNVs and CNAs obtained from whole genome sequencing data. CITUP (Malikic et al., ) proposes a combinatorial model for the problem of inferring clonal evolution from SNVs obtained from multiple tumor samples, and designs an exact algorithm based on a quadrati […]


Phylogenetic ctDNA analysis depicts early stage lung cancer evolution

PMCID: 5812436
PMID: 28445469
DOI: 10.1038/nature22364

[…] to represent tumor subclones, either current or ancestral, and are used as input for construction of phylogenetic relationship. Phylogenetic trees were primarily constructed using the published tool CITUP (0.1.0). However, in a small number of cases, including all relapse/autopsy cases, manual tree construction was required and performed as described. Complete detail of primary tumor tree constru […]


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CITUP institution(s)
School of Computing Science, Simon Fraser University, Burnaby, BC, Canada; BC Cancer Agency, Vancouver, BC, Canada; Vancouver Prostate Center, Vancouver, BC, Canada; School of Informatics and Computing, Indiana University, Bloomington, IN, USA

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