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Cancer evolution software tools | Phylogenomics

Cancer can be a result of accumulation of different types of genetic mutations such as copy number aberrations. The data from tumors are cross-sectional and do not contain the temporal order of the genetic events. Finding the order in which the…
TumourSimulator
Desktop

TumourSimulator

Simulates a model for tumour evolution that shows how short-range dispersal and…

Simulates a model for tumour evolution that shows how short-range dispersal and cell turnover can account for rapid cell mixing inside the tumour. TumourSimulator model shows that even a small…

deconstructSigs
Desktop

deconstructSigs

Allows the identification of mutational signatures within a single tumor…

Allows the identification of mutational signatures within a single tumor sample. The deconstructSigs approach determines the linear combination of pre-defined signatures that most accurately…

TiMEx
Desktop

TiMEx

A generative probabilistic model for detecting patterns of various degrees of…

A generative probabilistic model for detecting patterns of various degrees of mutual exclusivity across genetic alterations, which can indicate pathways involved in cancer progression. TiMEx…

fishplot
Desktop

fishplot

Displays changes in clonal structure over time. fishplot is able to produce…

Displays changes in clonal structure over time. fishplot is able to produce illustrative and easy-to-interpret graphs suitable for diagnosis, presentation, and publication. It permits to show how an…

TRONCO
Desktop

TRONCO TRanslational ONCOlogy

An open-source R package that implements the state-of-the-art algorithms for…

An open-source R package that implements the state-of-the-art algorithms for the inference of cancer progression models from (epi)genomic mutational profiles. TRONCO can be used to extract…

SIApopr
Desktop

SIApopr Simulating Infinite-Allele populations

Simulates homogeneous and inhomogeneous stochastic branching processes under a…

Simulates homogeneous and inhomogeneous stochastic branching processes under a very flexible set of assumptions. SIApopr simulates clonal evolution with the emergence of driver and passenger…

tumopp
Desktop

tumopp

Allows tumor growth simulation in C++. tumopp offers many setting options so…

Allows tumor growth simulation in C++. tumopp offers many setting options so that simulations can be carried out under various settings. Setting options include how the cell division rate is…

TO-DAG
Desktop

TO-DAG Timed Oncogenetic Directed Acyclic Graphs

Deduces from cross-sectional data of genetic alterations in tumor patients the…

Deduces from cross-sectional data of genetic alterations in tumor patients the causal dependencies and the waiting times among these genetic events. From matrices with genetic events and patient…

CAPRI
Desktop

CAPRI CAncer PRogression Inference

Relies on a scoring method based on a probabilistic theory developed by Suppes,…

Relies on a scoring method based on a probabilistic theory developed by Suppes, coupled with bootstrap and maximum likelihood inference. The resulting algorithm is efficient, achieves high accuracy…

Rtreemix
Desktop

Rtreemix

Offers an environment for estimating the mutagenetic trees mixture models from…

Offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. Rtreemix includes functions for fitting the trees mixture…

CPM-Cytoscape
Web

CPM-Cytoscape Cellular Potts Model Cytoscape

A comprehensive and expandable simulation tool to visualizing tumor growth.…

A comprehensive and expandable simulation tool to visualizing tumor growth. CPM-Cytoscape offers the advantage of a user-friendly graphical interface with several manipulable input variables to…

oncomodel
Desktop

oncomodel

An approach for modelling the dependences between genetic changes in human…

An approach for modelling the dependences between genetic changes in human tumours. oncomodel computes probabilistic tree models for oncogenesis based on genetic data using maximum likelihood. In…

SCHISM
Desktop

SCHISM SubClonal Hierarchy Inference from Somatic Mutations

Reconstructs tumor subclonal phylogenies using somatic mutation cellularities…

Reconstructs tumor subclonal phylogenies using somatic mutation cellularities in patient's tumor sample(s). SCHISM combines information about somatic mutation cellularity (aka mutation cancer…

phyC
Desktop

phyC Phylogenetic tree Clustering

A clustering method for cancer sub-clonal evolutionary trees, in which…

A clustering method for cancer sub-clonal evolutionary trees, in which sub-groups of the trees are identified based on topology and edge length attributes. phyC can detect true clusters with…

BML
Desktop

BML Bayesian Mutation Landscape

Reconstructs evolutionary paths and ancestral genotypes from sequenced tumor…

Reconstructs evolutionary paths and ancestral genotypes from sequenced tumor samples. BML first estimates the probability P(g) that a particular combination of mutations (denoted by genotype g)…

CT-CBN
Desktop

CT-CBN Continuous Time Conjunctive Bayesian Networks

A specific probabilistic graphical model for the accumulation of mutations and…

A specific probabilistic graphical model for the accumulation of mutations and their interdependencies. The Bayesian network models cancer progression by an explicit unobservable accumulation process…

Oncotree
Desktop

Oncotree

Estimating oncogenetic trees. Oncotree contains functions to construct and…

Estimating oncogenetic trees. Oncotree contains functions to construct and evaluate directed tree structures that model the process of occurrence of genetic alterations during carcinogenesis.

HPVbase
Dataset

HPVbase

A comprehensive resource for three major efficacious cancer biomarkers i.e.…

A comprehensive resource for three major efficacious cancer biomarkers i.e. integration and breakpoint events, human papillomaviruses (HPVs) methylation patterns and HPV mediated aberrant expression…

Mtreemix
Desktop

Mtreemix

A software package to estimate mixture models of mutagenetic trees from…

A software package to estimate mixture models of mutagenetic trees from observed cross-sectional data. Mutagenetic tree mixtures are probabilistic models that have been designed to describe…

DiProg
Desktop

DiProg

A software tool for learning disease progression networks by reducing to mixed…

A software tool for learning disease progression networks by reducing to mixed integer linear programming (MILP). In contrast to the semi-automatic method, DiProg is automatic and, therefore, needs…

Unmix
Desktop

Unmix

Performs mixture type separation on a tumor sample. Unmix approach uses…

Performs mixture type separation on a tumor sample. Unmix approach uses unmixing of tumor samples to assist in phylogenetic inference of cancer progression pathways. This unmixing method adapts the…

hotmix
Desktop

hotmix

This tool is used to generate hidden-variable oncogenetic trees (HOTs). The…

This tool is used to generate hidden-variable oncogenetic trees (HOTs). The trees are written using standard Newick notation, except that each vertex in the tree has a comment that describes the HOT…

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