HAPLO-IHP – Haplotype Inference using Identified Haplotype Patterns

SHIPS is a non-parametric clustering algorithm that clusters individuals from a population into genetically homogeneous sub-populations from genotype data.

::DEVELOPER

Matthieu Bouaziz <matthieu.x.bouaziz@gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/MacOsX
R package

:: DOWNLOAD

SHIPS

:: MORE INFORMATION

Citation

PLoS One. 2012;7(10):e45685. doi: 10.1371/journal.pone.0045685. Epub 2012 Oct 12.
SHIPS: Spectral Hierarchical clustering for the Inference of Population Structure in genetic studies.
Bouaziz M, Paccard C, Guedj M, Ambroise C.

GenoClone 0.1 – subClone inference and studying Tumor Heterogenity

GenoClone 0.1

:: DESCRIPTION

GenoClone aims to provide useful tool to infer the tumor subclones and study tumor heterogeneity.

::DEVELOPER

Au Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GenoClone

:: MORE INFORMATION

Citation

Zou M, Jin R, Au KF.
Revealing tumor heterogeneity of breast cancer by utilizing the linkage between somatic and germline mutations.
Brief Bioinform. 2019 Nov 27;20(6):2306-2315. doi: 10.1093/bib/bby084. PMID: 30239581; PMCID: PMC6954402.

sNMF 2.0 – Inference of Population Structure using Sparse Non-negative Matrix Factorization algorithms

sNMF 2.0

:: DESCRIPTION

sNMF (Sparse Non-negative Matrix Factorization) is a fast and efficient method for the inference of Admixture Coefficients.

::DEVELOPER

Eric Frichot

:: SCREENSHOTS

N/A

:: REQUIREMENTS

MacOsX / Linux

:: DOWNLOAD

sNMF

:: MORE INFORMATION

Citation

Genetics. 2014 Apr;196(4):973-83. doi: 10.1534/genetics.113.160572. Epub 2014 Feb 4.
Fast and efficient estimation of individual ancestry coefficients.
Frichot E1, Mathieu F, Trouillon T, Bouchard G, François O.

tigre 1.46.0 / tigreBrowser 1.1 – Transcription Factor Inference through Gaussian process Reconstruction of Expression

tigre 1.46.0 / tigreBrowser 1.1

:: DESCRIPTION

tigre is an R/Bioconductor package for inference of transcription factor activity and ranking candidate target genes from gene expression time series.

tigreBrowser is a web-based browser for tigre ranking results. It allows easy viewing, sorting and filtering of visualisations of models produced by tigre.

:: DEVELOPER

Antti Honkela

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / windows/ MacOsX
BioCOnductor
R package
Python

:: DOWNLOAD

tigre / tigreBrowser

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 1;27(7):1026-7. doi: 10.1093/bioinformatics/btr057. Epub 2011 Feb 7.
tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor.
Honkela A1, Gao P, Ropponen J, Rattray M, Lawrence ND.

SCG 0.3.1 – Inference of Clonal Genotypes

SCG 0.3.1

:: DESCRIPTION

SCG ( Single Cell Genotyper) is a software for inference of clonal genotypes using targeted single cell (nucleus) sequencing.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
Python

:: DOWNLOAD

SCG

:: MORE INFORMATION

Citation

Nat Methods. 2016 Jul;13(7):573-6. doi: 10.1038/nmeth.3867. Epub 2016 May 16.
Clonal genotype and population structure inference from single-cell tumor sequencing.
Roth A, McPherson A, Laks E, Biele J, Yap D, Wan A, Smith MA, Nielsen CB, McAlpine JN, Aparicio S, Bouchard-Côté A, Shah SP

CITUP v0.1.0 – Clonality Inference in Multiple Tumor Samples using Phylogeny

CITUP v0.1.0

:: DESCRIPTION

CITUP is a bioinformatics tool that can be used to infer tumor heterogeneity using multiple samples from a single patient. Given mutational frequencies for each sample, CITUP uses an optimization based algorithm to find the evolutionary tree best explaining the data.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
IBM ILOG CPLEX Optimization Studio

:: DOWNLOAD

CITUP

:: MORE INFORMATION

Citation

Clonality Inference in Multiple Tumor Samples using Phylogeny.
Malikic S, McPherson AW, Donmez N, Sahinalp CS.
Bioinformatics. 2015 Jan 6. pii: btv003.

GIGA 1.4.1 – Gene Tree Inference in the Genomic Age

GIGA 1.4.1

:: DESCRIPTION

GIGA is an efficient tree building program that allows phylogenetic reconstruction of very large gene families and determination of orthologs on a large scale. It is used to generate trees in the PANTHER Classification System.

::DEVELOPER

Paul D. Thomas

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX
C Compiler

:: DOWNLOAD

GIGA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Jun 9;11:312.
GIGA: a simple, efficient algorithm for gene tree inference in the genomic age.
Thomas PD.

treemix 1.13 – Inference of Population Trees with Admixture

treemix 1.13

:: DESCRIPTION

TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. We use the allele frequencies in the modern populations to infer the structure of this graph.

::DEVELOPER

Pritchard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

treemix

:: MORE INFORMATION

Citation:

Pickrell JK and Pritchard JK.
Inference of population splits and mixtures from genome-wide allele frequency data.
PLoS Genet 8(11): e1002967. doi:10.1371/journal.pgen.1002967

IsoInfer 0.9.1 – Inference of Isoforms from Short Sequence Reads

IsoInfer 0.9.1

:: DESCRIPTION

IsoInfer is a program to infer isoforms based on short RNA-Seq (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information.

::DEVELOPER

Wei Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C/C++ Compiler

:: DOWNLOAD

IsoInfer

:: MORE INFORMATION

Citation

J Comput Biol. 2011 Mar;18(3):305-21. doi: 10.1089/cmb.2010.0243.
Inference of isoforms from short sequence reads.
Feng J1, Li W, Jiang T.