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Tumor purity and clonality estimation software tools | Whole-genome sequencing data analysis

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…
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ABSOLUTE
Desktop

ABSOLUTE

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…

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PyClone
Desktop

PyClone

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…

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E-scape
Desktop

E-scape evolutionary landscapes

Renders complex relationships between cancer evolution data in an intuitive,…

Renders complex relationships between cancer evolution data in an intuitive, interactive framework for biomedical investigators. E-scape is composed of three visualization tools: TimeScape, MapScape,…

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deepSNV
Desktop

deepSNV

Provides quantitative variant callers for detecting subclonal mutations in…

Provides quantitative variant callers for detecting subclonal mutations in ultra-deep sequencing experiments. DeepSNV is a comparative targeted deep-sequencing approach combined with a customised…

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THetA
Desktop

THetA Tumor Heterogeneity Analysis

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…

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SynthEx
Desktop

SynthEx

Caters to the varying protocols of different next-generation sequencing…

Caters to the varying protocols of different next-generation sequencing protocols, to detect copy number alterations (CNAs). SynthEx uses a “synthetic-normal” strategy to correct for sample-specific…

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ExPANdS
Desktop

ExPANdS Expanding Ploidy and Allele Frequency on Nested Subpopulations

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…

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BubbleTree
Desktop

BubbleTree

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…

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MEDICC
Desktop

MEDICC Minimum Event Distance for Intra-tumour Copy-number Comparisons

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…

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ReMixT
Desktop

ReMixT

Tries to improve both inference and interpretation of copy number changes and…

Tries to improve both inference and interpretation of copy number changes and genomic rearrangements. ReMixT work about prediction of clone fraction, clone specific copy number, and clone specificity…

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PurBayes
Desktop

PurBayes

An MCMC-based algorithm that uses next-generation sequencing data to estimate…

An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.

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MuSE
Desktop

MuSE

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…

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HashClone
Web
Desktop

HashClone

Provides B-cells clonality assessment and Minimal Residual Disease (MRD)…

Provides B-cells clonality assessment and Minimal Residual Disease (MRD) monitoring over time. HashClone is a bioinformatics suite composed of four applications for data processing and one web…

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Canvas
Desktop

Canvas

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…

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CNAnorm
Desktop

CNAnorm

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…

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AbsCN-seq
Desktop

AbsCN-seq

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…

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GRAFT
Desktop

GRAFT Genomic Rearrangement Assembly For Tumours

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…

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BitPhylogeny
Desktop

BitPhylogeny

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…

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LICHeE
Desktop

LICHeE Lineage Inference for Cancer Heterogeneity and Evolution

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…

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PhyloWGS
Desktop

PhyloWGS

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…

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WSCUnmix
Desktop

WSCUnmix

Allows users to estimate and decompose mixture model substructure. WSCUnmix…

Allows users to estimate and decompose mixture model substructure. WSCUnmix assists in identification of substructure in parse, noisy data. It offers a method to several types of key model…

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ALOHA
Desktop

ALOHA Allele-frequency/Loss-Of-Heterozygosity/Allele-imbalance

Extracts hidden genetic information and broaden the potential application of…

Extracts hidden genetic information and broaden the potential application of allele frequency to genomic research. ALOHA can detect loss of heterozygosity (LOH) and recognize allelic imbalance (AI).…

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PurityEst
Desktop

PurityEst

A computational tool for estimating purity of human tumor samples using…

A computational tool for estimating purity of human tumor samples using next-generation sequencing data.

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PyLOH
Desktop

PyLOH

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.

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CLONET
Desktop

CLONET CLONality Estimate in Tumors

Quantifies the percentage of reads supporting a considered aberration from…

Quantifies the percentage of reads supporting a considered aberration from clinical tumors. CLONET uses the abundant germline heterozygous SNP genotype data provided by whole genome sequence coverage…

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Sequenza
Desktop

Sequenza

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…

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TrAp
Desktop

TrAp Tree Approach

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…

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PureCN
Desktop

PureCN

Estimates tumor purity, copy number, loss of heterozygosity (LOH), and status…

Estimates tumor purity, copy number, loss of heterozygosity (LOH), and status of single nucleotide variants (SNVs). PureCN is designed for targeted short read sequencing data, integrates well with…

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Canopy
Desktop

Canopy

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…

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QuantumClone
Desktop

QuantumClone

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…

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GLAD
Desktop

GLAD

Serves for the genomic classification of solid tumors. GLAD is a statistical…

Serves for the genomic classification of solid tumors. GLAD is a statistical model that estimates a per-sample distribution over subtypes and makes an all-or-none classification for each sample. It…

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PBS
Desktop

PBS Pathway Based Distance Score

Assesses the biological differences between samples using gene expression data.…

Assesses the biological differences between samples using gene expression data. PBS uses gene expression data by assuming that ontologically defined biological pathways in biologically similar…

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TITAN
Desktop

TITAN

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…

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Subcloneseeker
Desktop

Subcloneseeker

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…

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Clomial
Desktop

Clomial

Incorporates information from multiple sections from a single tumor at a single…

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 important difference between…

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HetFHMM
Algorithm

HetFHMM Factorial Hidden Markov Model for analyzing heterogeneity

Allows users to identify tumor clones and tumor samples based on factorial…

Allows users to identify tumor clones and tumor samples based on factorial hidden Markov models (HMM). HetFHMM uses next generation sequencing (NGS) short reads to detect clonal frequency, type of…

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scploid
Desktop

scploid Single Cell RNA-seq Aneuploidy Caller

Provides an approach for aneuploidies calling in single-cell RNA-sequencing.…

Provides an approach for aneuploidies calling in single-cell RNA-sequencing. scploid is an R package performing for each cell, the identification of chromosomes including genes with potentially…

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BayCount
Desktop

BayCount

Infers tumor transcriptional heterogeneity using RNA-Seq count data. BayCount…

Infers tumor transcriptional heterogeneity using RNA-Seq count data. BayCount is a Bayesian matrix decomposition model that takes into account both random effects between samples and specific genetic…

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PDAC Disease Models
Desktop

PDAC Disease Models Pancreatic Ductal AdenoCarcinoma Disease Models

Provides a pipeline for analyzing whole-genome sequencing (WGS) data for simple…

Provides a pipeline for analyzing whole-genome sequencing (WGS) data for simple somatic mutation (SSM), structural variation (SV) and copy number variation (CNV). PDAC Disease Models is a R package…

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cancerTiming
Desktop

cancerTiming

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…

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FISHtrees
Desktop

FISHtrees

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…

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AncesTree
Desktop

AncesTree

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…

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CNALR
Desktop

CNALR

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…

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CITUP
Desktop

CITUP Clonality Inference in Tumors Using Phylogeny

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…

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TumorTracer
Web

TumorTracer

Identifies the tissue origin from the somatic mutations of a tumor specimen.…

Identifies the tissue origin from the somatic mutations of a tumor specimen. TumorTracer uses the point mutation and copy number status of a set of 232 genes recurrently mutated in cancer, as well as…

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TuMult
Desktop

TuMult

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…

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cloneHD
Desktop

cloneHD

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…

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MixedPerfectPhy…
Desktop

MixedPerfectPhylogeny

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…

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SPRUCE
Desktop

SPRUCE Somatic Phylogeny Reconstruction Using Combinatorial Enumeration

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…

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rec-BTP
Desktop

rec-BTP Binary Tree Partition

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…

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CLImAT
Desktop

CLImAT CAN and LOH Assessment in Impure and Aneuploid Tumors

A bioinformatic tool for identification of genome-wide aberrations from tumor…

A bioinformatic tool for identification of genome-wide aberrations from tumor samples using whole-genome sequencing data.

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CaPSID
Desktop

CaPSID Computational Pathogen Sequence IDentification

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…

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SCUnmix
Desktop

SCUnmix

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…

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SciClone
Desktop

SciClone

Infers the subclonal architecture of tumors. SciClone is a method for…

Infers the subclonal architecture of tumors. SciClone is a method for estimating the number and content of subclones across one or many samples. It focuses primarily on variants in copy-number…

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Cellscape
Desktop

Cellscape

Facilitates interactive research of single cell clonal evolution datasets.…

Facilitates interactive research of single cell clonal evolution datasets. Cellscape returns an interactive single cell phylogeny and a cell-by-locus genomic heatmap.

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Timescape
Desktop

Timescape

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…

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MapScape
Desktop

MapScape

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…

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Bayclone
Desktop

Bayclone

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…

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Muttree
Desktop

Muttree

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…

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PhyloSub
Desktop

PhyloSub

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…

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qpure
Desktop

qpure

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…

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ISOLATE
Desktop

ISOLATE

Identifies sites of origin by latent variables. ISOLATE has three goals: (1)…

Identifies sites of origin by latent variables. ISOLATE has three goals: (1) detection of the site of origin from a set of profiled candidate sites, (2) de-convolution of heterogeneous expression…

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