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

 NO

:: 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.

TSCAN 1.7.0 – Pseudo-time Reconstruction and Evaluation in Single-cell RNA-seq Analysis

TSCAN 1.7.0

:: DESCRIPTION

TSCAN (Tools for Single-Cell ANalysis) is a software tool developed to better support in silico pseudo-Time reconstruction in Single-Cell RNA-seq ANalysis.

::DEVELOPER

Zhicheng Ji

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 TSCAN

:: MORE INFORMATION

Citation

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis.
Ji Z, Ji H.
Nucleic Acids Res. 2016 May 13. pii: gkw430.

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

  NO

:: 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.

methylFlow – Cell-specific Methylation Pattern Reconstruction

methylFlow

:: DESCRIPTION

methylFlow is a software of cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing.

::DEVELOPER

HCBravo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 methylFlow

:: MORE INFORMATION

Citation

methylFlow: cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing.
Dorri F, Mendelowitz L, Corrada Bravo H.
Bioinformatics. 2016 Jun 1;32(11):1618-24. doi: 10.1093/bioinformatics/btw287

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.

Jane 4.01 – Cophylogeny Reconstruction

Jane 4.01

:: DESCRIPTION

Jane is a software tool for the cophylogeny reconstruction problem.

::DEVELOPER

Professor Ran Libeskind-Hadas

:: SCREENSHOTS

Jane

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • JRE

:: DOWNLOAD

 Jane

:: MORE INFORMATION

Citation

Jane: a new tool for the cophylogeny reconstruction problem.
Conow C, Fielder D, Ovadia Y, Libeskind-Hadas R.
Algorithms Mol Biol. 2010 Feb 3;5:16. doi: 10.1186/1748-7188-5-16.