Tag: Reconstruction

iARG – Imperfect Ancestral Recombination Graph Reconstruction

iARG

:: DESCRIPTION

iARG is a collection of tools to reconstruct evolutionary histories which include recombination and back/recurrent mutation events.

::DEVELOPER

The Istrail Laboratory of Brown University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • C++ Compiler

:: DOWNLOAD

 iARG

:: MORE INFORMATION

Citation

J Comput Biol. 2010 Jun;17(6):767-81. doi: 10.1089/cmb.2009.0249.
The imperfect ancestral recombination graph reconstruction problem: upper bounds for recombination and homoplasy.
Lam F1, Tarpine R, Istrail S.

TreeClone v1 – Reconstruction of Tumor Subclone Phylogeny Based on Mutation Pairs using Next Generation Sequencing Data

TreeClone v1

:: DESCRIPTION

TreeClone is a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution.

::DEVELOPER

Yuan Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

TreeClone

:: MORE INFORMATION

Citation

[Submitted on 10 Mar 2017 (v1), last revised 25 Oct 2017 (this version, v2)]
TreeClone: Reconstruction of Tumor Subclone Phylogeny Based on Mutation Pairs using Next Generation Sequencing Data
Tianjian Zhou, Subhajit Sengupta, Peter Mueller, Yuan Ji

ECLAIR – Robust Lineage Reconstruction from Single-cell Gene Expression data

ECLAIR

:: DESCRIPTION

ECLAIR (Ensemble Clustering for Lineage Analysis, Inference and Robustness) achieves a higher level of confidence in the estimated lineages through the use of approximation algorithms for consensus clustering and by combining the information from an ensemble of minimum spanning trees so as to come up with an improved, aggregated lineage tree.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python

:: DOWNLOAD

ECLAIR

:: MORE INFORMATION

Citation

Giecold G, Marco E, Trippa L, Yuan GC.
Robust Lineage Reconstruction from High-Dimensional Single-Cell Data.
Nucleic Acids Res. 2016 May 20. pii: gkw452.

PICRUSt2 v2.3.0-b -Phylogenetic Investigation of Communities by Reconstruction of Unobserved States

PICRUSt2 v2.3.0-b

:: DESCRIPTION

PICRUSt is a software for predicting functional abundances based only on marker gene sequences.

::DEVELOPER

PICRUSt2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PICRUSt2

:: MORE INFORMATION

Citation

PICRUSt2: An improved and extensible approach for metagenome inference
Gavin M. Douglas, Vincent J. Maffei, Jesse Zaneveld, Svetlana N. Yurgel, James R. Brown, Christopher M. Taylor, Curtis Huttenhower, Morgan G. I. Langille
doi: https://doi.org/10.1101/672295

SPIMAP 1.1 – Species Informed Maximum A Posteriori Gene Tree Reconstruction

SPIMAP 1.1

:: DESCRIPTION

SPIMAP is a phylogenetic reconstruction method specifically designed for reconstructing gene trees in the case of a known species tree.

::DEVELOPER

Matt Rasmussen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler
  • Python

:: DOWNLOAD

 SPIMAP 

:: MORE INFORMATION

Citation

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction
Matthew D. Rasmussen and Manolis Kellis.
Mol Biol Evol (2011) 28 (1): 273-290.

CytoTRACE beta – Cellular (Cyto) Trajectory Reconstruction Analysis using gene Counts and Expression

CytoTRACE beta

:: DESCRIPTION

CytoTRACE is a computational method to predict the differentiation states of cells from single-cell RNA-sequencing data, without prior knowledge of developmental orderings

::DEVELOPER

Newman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

CytoTRACE

:: MORE INFORMATION

Citation

Science, 367 (6476), 405-411 2020 Jan 24
Single-cell Transcriptional Diversity Is a Hallmark of Developmental Potential
Gunsagar S Gulati et al.

CARMEN – Comparative Analysis and Reconstruction of MEtabolic Network

CARMEN

:: DESCRIPTION

The software CARMEN was developed to support functional and comparative genome analysis. CARMEN provides the visualization of automatically obtained metabolic networks based on KEGG database information and stores the generated data in standardized SBML format. SBML is an open source XML-based format that facilitates the description of models and their exchange between various simulation and analysis tools

::DEVELOPER

CARMEN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 CARMEN

:: MORE INFORMATION

Citation

CARMEN – Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks.
Schneider J, Vorhölter FJ, Trost E, Blom J, Musa YR, Neuweger H, Niehaus K, Schatschneider S, Tauch A, Goesmann A.
Genet Mol Res. 2010 Aug 24;9(3):1660-72. doi: 10.4238/vol9-3gmr901.

RTN 2.10.1 – Reconstruction and Analysis of Transcriptional Networks

RTN 2.10.1

:: DESCRIPTION

RTN provides classes and methods for transcriptional network inference and and analysis.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

 RTN

:: MORE INFORMATION

Citation

Nat Commun. 2013;4:2464. doi: 10.1038/ncomms3464.
Master regulators of FGFR2 signalling and breast cancer risk.
Fletcher MN1, Castro MA, Wang X, de Santiago I, O’Reilly M, Chin SF, Rueda OM, Caldas C, Ponder BA, Markowetz F, Meyer KB.

tREX – Reconstruction of 3D structure of Chromatins using Hi-C data

tREX

:: DESCRIPTION

tPAM and tREX(truncated Random effect EXpression) are codes for reconstruction of 3D structure of chromatins using Hi-C data based on two model-based algorithms.

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

tREX

:: MORE INFORMATION

Citation

BMC Bioinformatics, 17, 70 2016 Feb 6
Impact of Data Resolution on Three-Dimensional Structure Inference Methods
Jincheol Park, Shili Lin

HapTree-X v1.0 – Haplotype Reconstruction tool Tailored towards RNA-seq Reads

HapTree-X v1.0

:: DESCRIPTION

HapTree-X is a haplotype reconstruction tool tailored towards phasing experiments with RNA-seq reads (by itself or jointly with genome/exome sequencing reads).

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

HapTree-X

:: MORE INFORMATION

Citation:

Res Comput Mol Biol, 9029, 28-29 2015
HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction From Transcriptome and Genome Sequencing Data
Emily Berger, Deniz Yorukoglu, Bonnie Berger

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