Solid tumor samples typically contain multiple distinct clonal populations of cancer cells, and also stromal and immune cell contamination. A majority of the cancer genomics and transcriptomics studies do not explicitly consider genetic heterogeneity and impurity, and draw…

Solid tumor samples typically contain multiple distinct clonal populations of cancer cells, and also stromal and immune cell contamination. A majority of the cancer genomics and transcriptomics studies do not explicitly consider genetic heterogeneity and impurity, and draw inferences based on mixed populations of cells. Deconvolution of genomic data from heterogeneous samples provides a powerful tool to address this limitation.

Infers tumor purity and malignant cell ploidy directly from analysis of somatic…

Infers tumor purity and malignant cell ploidy directly from analysis of somatic DNA alterations. ABSOLUTE can detect subclonal heterogeneity, somatic homozygosity, and calculate statistical…

A tool for inferring the cellular frequency of point mutations from deeply…

A tool for inferring the cellular frequency of point mutations from deeply sequenced data. The model supports simultaneous analysis of multiple related samples and infers clusters of mutations whose…

An algorithm that estimates the tumor purity and clonal/subclonal copy number…

An algorithm that estimates the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. THetA successfully estimates normal admixture and recovers…

Characterizes coexisting subpopulations in a single tumor sample using copy…

Characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data. The model detects coexisting…

An intuitive representation of purity, allele-specific copy number, and…

An intuitive representation of purity, allele-specific copy number, and clonality for human tumor specimens. BubbleTree displays the clonal composition within a tumor at the genomic segment level…

A method for phylogenetic reconstruction and heterogeneity quantification based…

A method for phylogenetic reconstruction and heterogeneity quantification based on a minimum event distance for intra-tumour copy-number comparisons. Given multiple such evolutionarily-related…

A somatic point mutation caller for tumor-normal paired samples in…

A somatic point mutation caller for tumor-normal paired samples in next-generation sequencing (NGS) data. MuSE models the evolution of the reference allele to the allelic composition of the matched…

A normalization method for copy number aberration in cancer samples. CNAnorm…

A normalization method for copy number aberration in cancer samples. CNAnorm performs ratio, GC content correction and normalization of data obtained using very low coverage (one read every…

A simple and robust algorithm to infer purity, ploidy and absolute copy numbers…

A simple and robust algorithm to infer purity, ploidy and absolute copy numbers in whole numbers for tumor cells from sequencing data. A simulation study shows that estimates have reasonable…

A technique to help reconstruct the history of rearrangements responsible for…

A technique to help reconstruct the history of rearrangements responsible for cancer genome karyotypes. This uses allelic copy number segmentation, rearrangements, and somatic single-nucleotide…

A probabilistic framework to reconstruct intra-tumor evolutionary pathways. The…

A probabilistic framework to reconstruct intra-tumor evolutionary pathways. The statistical model is based on simultaneously assigning markers of evolution to clones, which are represented as both…

Automates the phylogenetic inference of cancer progression from multiple…

Automates the phylogenetic inference of cancer progression from multiple somatic samples. LICHeE uses variant allele frequencies of somatic single nucleotide variants obtained by deep sequencing to…

A method that can be applied to WGS data from one or more tumor samples to…

A method that can be applied to WGS data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations and…

A model to resolve the identifiability problem by integrating two types of…

A model to resolve the identifiability problem by integrating two types of sequencing information - somatic copy number alterations and loss of heterozygosity.

Cancer arises from initiating cells (clones) that undergo intense evolutionary…

Cancer arises from initiating cells (clones) that undergo intense evolutionary selection during disease progression and can be widely altered during treatment. The tumor cell evolutionary process may…

A software package that uses paired tumor-normal DNA sequencing data to…

A software package that uses paired tumor-normal DNA sequencing data to estimate tumor cellularity and ploidy, and to calculate allele-specific copy number profiles and mutation profiles. Comparison…

An evolutionary framework for deconvolving data from a single genome-wide…

An evolutionary framework for deconvolving data from a single genome-wide experiment to infer the composition, abundance and evolutionary paths of the underlying cell subpopulations of a tumor. TrAp…

A statistical framework and computational procedure for identifying the…

A statistical framework and computational procedure for identifying the sub-populations within a tumor, determining the mutation profiles of each subpopulation, and inferring the tumor's…

Clusters variants into clones. QuantumClone applies an expectation-maximization…

Clusters variants into clones. QuantumClone applies an expectation-maximization (EM) algorithm and allows for accurate inference of clonal structure using Variant Allele Frequencies (VAFs) from one…

A tool for identification of copy number changes from diverse sequencing…

A tool for identification of copy number changes from diverse sequencing experiments including whole-genome matched tumor-normal and single-sample normal re-sequencing, as well as whole-exome matched…

A tool for predicting subclonal copy number alterations (CNA) and loss of…

A tool for predicting subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) from tumour whole genome sequencing data. It infers the clonal cluster of events along with their…

Examines somatic variation events (such as copy number changes, loss of…

Examines somatic variation events (such as copy number changes, loss of heterozygosity, or point mutations) in order to identify the underlying subclone structure, i.e. the subclones including the…

A generative binomial model that incorporates information from multiple…

A generative binomial model that incorporates information from multiple sections from a single tumor at a single time point to infer the frequencies and genotypes for a specified number of clones. An…

A maximum-likelihood estimation procedure that fully accounts for sequencing…

A maximum-likelihood estimation procedure that fully accounts for sequencing variability and show that it outperforms the partial maximum-likelihood estimation method. A Bayesian estimation procedure…

A framework for inferring models of tumor progression from single-cell gene…

A framework for inferring models of tumor progression from single-cell gene copy number data, including variable rates for different gain and loss events. Application of FISHtrees to real cervical…

Infers the clonal evolution and tumor composition, including mixing fractions,…

Infers the clonal evolution and tumor composition, including mixing fractions, of a tumor from multi-sample DNA sequence data. AncesTree is better able to identify ancestral relationships between…

An R package to perform a stratification of tumour subtypes based on copy…

An R package to perform a stratification of tumour subtypes based on copy number alteration profiles using next-generation sequence data. CNALR exhibits the best agreement in the prediction between…

A combinatorial method that infers clonal populations and their frequencies…

A combinatorial method that infers clonal populations and their frequencies while satisfying phylogenetic constraints and is able to exploit data from multiple samples. Using simulated datasets and…

A computational method for reconstructing the sequence of copy number changes…

A computational method for reconstructing the sequence of copy number changes driving carcinogenesis, based on the analysis of several tumor samples from the same patient. TuMult is a valuable tool…

A software tool for reconstructing the subclonal structure of a population from…

A software tool for reconstructing the subclonal structure of a population from short-read sequencing data. Read depth data, B-allele count data and somatic nucleotide variant (SNV) data can be used…

Contains methods for the MINIMUM CONFLICT-FREE ROW SPLIT problem.…

Contains methods for the MINIMUM CONFLICT-FREE ROW SPLIT problem. MixedPerfectPhylogeny assembles the implementations of two algorithms: an efficient heuristic algorithm based on coloring…

Infers a multi-state perfect phylogeny describing the evolutionary history of…

Infers a multi-state perfect phylogeny describing the evolutionary history of the somatic mutations (Single-Nucleotide Variations (SNV)s and Copy-Number Aberrations (CNAs)) of a tumor given…

A combinatorial formulation of the problem of constructing the subpopulations…

A combinatorial formulation of the problem of constructing the subpopulations of tumor cells from the variant allele frequencies of somatic mutations. BTP outperforms existing clustering approaches…

Identifies, queries and visualizes both exogenous and endogenous pathogen…

Identifies, queries and visualizes both exogenous and endogenous pathogen nucleotide sequences in tumor genomes and transcriptomes. CaPSID integrates a high-performance computational pipeline for…

A method for deconvoluting mixtures of genomic data with the goal of more…

A method for deconvoluting mixtures of genomic data with the goal of more accurately reconstructing cellular progression processes from bulk tumor genomic data. The method is designed to take better…

Provides an automated tool for navigating temporal clonal evolution data.…

Provides an automated tool for navigating temporal clonal evolution data. Timescape allows users to study the enumeration of clones, their evolutionary relationships and their shifting dynamics over…

Provides interactive visualization of spatial clonal evolution. MapScape…

Provides interactive visualization of spatial clonal evolution. MapScape integrates clonal prevalence, clonal hierarchy, anatomic and mutational information. It can accept a data table of mutations…

An allocation model to describe tumor heterogeneity (TH) using next-generation…

An allocation model to describe tumor heterogeneity (TH) using next-generation sequencing (NGS) data. Taking a Bayesian approach, the Indian buffet process (IBP) is extended to define a class of…

Infers an evolutionary mutation tree based on single cell sequencing data.…

Infers an evolutionary mutation tree based on single cell sequencing data. Muttree differs from traditional phylogenetic tree approaches in that mutation tree directly describes temporal order…

A statistical model that infers the phylogeny and genotype of the major…

A statistical model that infers the phylogeny and genotype of the major subclonal lineages represented in the population of cancer cells. It uses a Bayesian nonparametric prior over trees that groups…

Estimates tumour cellularity in samples to be used for cancer genomic studies…

Estimates tumour cellularity in samples to be used for cancer genomic studies where the presence of normal tissue in the tumor sample can significantly affect downstream analyses. qpure is an…