LICHeE 1.0 – Multi-sample Cancer Phylogeny Reconstruction

LICHeE 1.0

:: DESCRIPTION

LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution) is a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples.

::DEVELOPER

Serafim’s Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Java Runtime Environment (JRE)

:: DOWNLOAD

 LICHeE

:: MORE INFORMATION

Citation

Fast and scalable inference of multi-sample cancer lineages.
Popic V, Salari R, Hajirasouliha I, Kashef-Haghighi D, West RB, Batzoglou S.
Genome Biol. 2015 May 6;16(1):91

FastML 201401 – Server for computing Maximum Likelihood Ancestral Sequence Reconstruction

FastML 201401

:: DESCRIPTION

The FastML server is a bioinformatics tool for the reconstruction of ancestral sequences based on the phylogenetic relations between homologous sequences.

:: DEVELOPER

Edmond J. Safra Center for Bioinformatics  at Tel-Aviv university.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FastML

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W580-4. doi: 10.1093/nar/gks498. Epub 2012 May 31.
FastML: a web server for probabilistic reconstruction of ancestral sequences.
Ashkenazy H1, Penn O, Doron-Faigenboim A, Cohen O, Cannarozzi G, Zomer O, Pupko T.

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.

PhISCS 1.0 – Tumor Phylogeny Reconstruction via Integrative use of Single Cell and Bulk Sequencing Data

PhISCS 1.0

:: DESCRIPTION

PhISCS is a tool for sub-perfect tumor phylogeny reconstruction via integrative use of single cell and bulk sequencing data.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PhISCS

:: MORE INFORMATION

Citation

Malikic S, Mehrabadi FR, Ciccolella S, Rahman MK, Ricketts C, Haghshenas E, Seidman D, Hach F, Hajirasouliha I, Sahinalp SC.
PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data.
Genome Res. 2019 Nov;29(11):1860-1877. doi: 10.1101/gr.234435.118. Epub 2019 Oct 18. PMID: 31628256; PMCID: PMC6836735.

PRIMUS 1.8.0 – Pedigree Reconstruction and Identification of a Maximum Unrelated Set

PRIMUS 1.8.0

:: DESCRIPTION

PRIMUS is a pedigree reconstruction algorithm that uses estimates of genome-wide identity by descent to reconstruct pedigrees consistent with observed genetic data.

::DEVELOPER

PRIMUS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 PRIMUS

:: MORE INFORMATION

Citation

PRIMUS: Improving Pedigree Reconstruction using Mitochondrial and Y Haplotypes.
Staples J, Ekunwe L, Lange E, Wilson JG, Nickerson DA, Below JE.
Bioinformatics. 2015 Oct 29. pii: btv618

CoRegNet 1.30.0 – Reconstruction and Integrated Analysis of Co-regulatory Networks

CoRegNet 1.30.0

:: DESCRIPTION

COREGNET is an R/Bioconductor package to analyze large-scale transcriptomic data by highlighting sets of co-regulators.

::DEVELOPER

Remy Nicolle <remy.c.nicolle at gmail.com>,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 COREGNET

:: MORE INFORMATION

Citation

COREGNET: reconstruction and integrated analysis of co-regulatory networks.
Nicolle R, Radvanyi F, Elati M.
Bioinformatics. 2015 May 14. pii: btv305.

MOGEN 1.0 – 3D Genome Reconstruction

MOGEN 1.0

:: DESCRIPTION

MOGEN is a useful tool for converting chromosomal contact data into 3D genome models to provide a better view into the spatial organization of genomes.

::DEVELOPER

Jianlin Jack Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MOGEN

:: MORE INFORMATION

Citation

MOGEN: A Tool for Reconstructing 3D Models of Genomes from Chromosomal Conformation Capturing Data.
Trieu T, Cheng J.
Bioinformatics. 2015 Dec 31. pii: btv754

Arboretum – Reconstruction and analysis of Evolutionary History of Condition-specific Transcriptional Modules

Arboretum

:: DESCRIPTION

Arboretum is a novel scalable computational algorithm that integrates expression data from multiple species with species and gene phylogenies to infer modules of coexpressed genes in extant species and their evolutionary histories.

::DEVELOPER

Roy Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Arboretum

:: MORE INFORMATION

Citation

Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules.
Roy S, Wapinski I, Pfiffner J, French C, Socha A, Konieczka J, Habib N, Kellis M, Thompson D, Regev A.
Genome Res. 2013 Jun;23(6):1039-50. doi: 10.1101/gr.146233.112.

CIRCLET – Circular Trajectory Reconstruction tool

CIRCLET

:: DESCRIPTION

CIRCLET is a powerful and robust circular trajectory reconstruction tool without specifying a starting cell for resolving cell cycle phases of single cells by considering multi-scale features of chromosomal architectures. CIRCLET reveals its best superiority based on the combination of a feature set about global information and two feature sets about local interactional information in terms of designed evaluation indexes and verification strategies from a collection of cell cycle Hi-C maps.

::DEVELOPER

Shihua Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

CIRCLET

:: MORE INFORMATION

Citation

Ye Y, Gao L, Zhang S.
Circular Trajectory Reconstruction Uncovers Cell-Cycle Progression and Regulatory Dynamics from Single-Cell Hi-C Maps.
Adv Sci (Weinh). 2019 Sep 30;6(23):1900986. doi: 10.1002/advs.201900986. PMID: 31832309; PMCID: PMC6891923.

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