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

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.

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

PhosNetConstruct – Phosphorylation Network Reconstruction

PhosNetConstruct

:: DESCRIPTION

PhosNetConstruct is a tool to predict novel phosphorylation networks based on the preference of certain kinase families to phosphorylate specific functional protein families (domains). It identifies the potentially phosphorylated proteins from a given set of proteins and predicts target kinases which in turn would phosphorylate these identified phosphoproteins based on their domain compositions.

::DEVELOPER

PhosNetConstruct team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):1730-8. doi: 10.1093/bioinformatics/btu112. Epub 2014 Feb 25.
Deciphering kinase-substrate relationships by analysis of domain-specific phosphorylation network.
Damle NP, Mohanty D.

SubcloneSeeker 1.0.0 – Computational Reconstruction of Tumor Clones

SubcloneSeeker 1.0.0

:: DESCRIPTION

SubcloneSeeker is a software framework, that 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 normal (non-cancerous) cells and their cellular frequencies within the tumor tissue.

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SubcloneSeeker

:: MORE INFORMATION

Citation

Genome Biol. 2014 Aug 26;15(8):443. doi: 10.1186/s13059-014-0443-x.
SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization.
Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth GT.

FastME 2.1.5 – Fast & Accurate Phylogeny Reconstruction

FastME 2.1.5

:: DESCRIPTION

FastME is a software for fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. FastME showed better topological accuracy than NJ, BIONJ, WEIGHBOR and FITCH, in all evolutionary conditions we tested, which include large range deviations from molecular clock and substitution rates. When the number of taxa is high, its superiority over NJ, BIONJ and WEIGHBOR becomes important, while FITCH remains close to FastME but becomes hard to use due to its slowness. FastME is very fast, even faster than NJ, and can easily be applied to very large data sets (> 1000 taxa).

::DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

FastME

:: MORE INFORMATION

Citation

Mol Biol Evol. 2015 Oct;32(10):2798-800. doi: 10.1093/molbev/msv150. Epub 2015 Jun 30.
FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program.
Lefort V, Desper R, Gascuel O

Desper R., Gascuel O.
Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle.
Journal of Computational Biology. 2002 9(5):687-705.

IQ-TREE 1.6.12 / W-IQ-TREE – Efficient Phylogenetic Tree Reconstruction and ultrafast Bootstrap Approximation

IQ-TREE 1.6.12 / W-IQ-TREE

:: DESCRIPTION

IQ-TREE is a very efficient phylogenetic software for reconstructing maximum-likelihood trees and assessing branch supports with the ultrafast bootstrap approximation. It is based on the IQPNNI algorithm with 10-fold speedup together with substantially additional features.

W-IQ-TREE is an intuitive and user-friendly web interface and server for IQ-TREE

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 IQ-TREE

:: MORE INFORMATION

Citation

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis.
Trifinopoulos J, Nguyen LT, von Haeseler A, Minh BQ.
Nucleic Acids Res. 2016 Apr 15. pii: gkw256.

Bui Quang Minh, Minh Anh Thi Nguyen, and Arndt von Haeseler (2013)
Ultrafast approximation for phylogenetic bootstrap.
Mol. Biol. Evol.,doi: 10.1093/molbev/mst024

EAGER 1.92.37 – Efficient Ancient Genome Reconstruction

EAGER 1.92.37

:: DESCRIPTION

EAGER is a time-efficient pipeline, which greatly simplifies the analysis of large-scale genomic data sets. EAGER provides features to preprocess, map, authenticate, and assess the quality of ancient DNA samples. Additionally, EAGER comprises tools to genotype samples to discover, filter, and analyze variants.

::DEVELOPER

Research Group “Integrative Transcriptomics” , Center for Bioinformatics Tübingen, University of Tübingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOS

:: DOWNLOAD

EAGER

:: MORE INFORMATION

Citation

A. Peltzer; G. Jäger; A. Herbig; S. Seitz; C. Kniep; J. Krause; K. Nieselt
EAGER: efficient ancient genome reconstruction
Genome Biology 2016, 17:60, doi:10.1186/s13059-016-0918-z

MinPath 1.4 – Biological Pathway Reconstructions using Protein Family Predictions

MinPath 1.4

:: DESCRIPTION

MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 MinPath

:: MORE INFORMATION

Citation:

Yuzhen Ye and Thomas G. Doak.
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.
PLoS Computational Biology, 5(8): e1000465 (2009)