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

:: 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)

RNAfitme – Reconstruction & Remodeling of Full-Atom RNA Structure

RNAfitme

:: DESCRIPTION

RNAfitme is a webserver to reconstruct full-atomic RNA 3D structure based on sequence and fixed sugar-phopshate backbone, remodel the structure, and reduce steric clashes.

::DEVELOPER

The Bioinformatics Group, Poznan University of Technology.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2018 Aug 22;19(1):304. doi: 10.1186/s12859-018-2317-9.
RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures.
Antczak M, Zok T, Osowiecki M, Popenda M, Adamiak RW, Szachniuk M.

SHOT 2.0 – Shared Ortholog and Gene Order Tree Reconstruction Tool

SHOT 2.0

:: DESCRIPTION

SHOT is a web server for the classification of genomes on the basis of shared gene content or the conservation of gene order that reflects the dominant, phylogenetic signal in these genomic properties. In general, the genome trees are consistent with classical gene-based phylogenies, although some interesting exceptions indicate massive horizontal gene transfer. SHOT is a useful tool for analysing the tree of life from a genomic point of view

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

SHOT: a web server for the construction of genome phylogenies.
Korbel JO, Snel B, Huynen MA, Bork P
Trends Genet. 2002 Mar; 18(3): 158-62. PubMed: 11858840.

NeuronStudio 0.9.92 – Reconstruction of Neuronal Structures from Confocal and Multi-photon Images

NeuronStudio 0.9.92

:: DESCRIPTION

NeuronStudio is designed to allow reconstruction of neuronal structures from confocal and multi-photon images.

::DEVELOPER

Computational Neurobiology and Imaging Center

:: SCREENSHOTS

:: REQUIREMENTS

WIndows

:: DOWNLOAD

NeuronStudio

:: MORE INFORMATION

Citation

Rodriguez A., Ehlenberger D.B., Dickstein D.L., Hof P.R., Wearne S.L.
Automated Three-Dimensional Detection and Shape Classification of Dendritic Spines from Fluorescence Microscopy Images.
PLoS ONE 3(4): e1997 doi:10.1371/journal.pone.0001997 (2008).

FRANz 2.0 – Reconstruction of Pedigrees

FRANz 2.0

:: DESCRIPTION

FRANz is a fast and flexible parentage inference program for natural populations.

::DEVELOPER

Bioinformatics Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/windows/MacOsX

:: DOWNLOAD

FRANz

:: MORE INFORMATION

Citation

FRANz: Reconstruction of wild multi-generation pedigrees.
Markus Riester, Peter F Stadler, Konstantin Klemm.
Bioinformatics. 2009. 25:2134-2139.