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|Alternative name||Clonality Inference in Tumors Using Phylogeny|
|Interface||Command line interface|
|Restrictions to use||None|
No version available
- person_outline S. Cenk Sahilp
Publication for Clonality Inference in Tumors Using Phylogeny
Genetic Evidence for Early Peritoneal Spreading in Pelvic High Grade Serous Cancer
[…] 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
[…] 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
[…] 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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