GEIGER 2.0.7 – Analysis of Evolutionary Diversification

GEIGER 2.0.7

:: DESCRIPTION

GEIGER is an R package for the comparative analysis of evolutionary radiations.

::DEVELOPER

Harmon Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R

:: DOWNLOAD

  GEIGER

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 7. [Epub ahead of print]
geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees.
Pennell MW1, Eastman JM, Slater GJ, Brown JW, Uyeda JC, Fitzjohn RG, Alfaro ME, Harmon LJ.

LumberJack 7.10 – Analyzing the Phylogenetic Signal in Regions of Multiple Sequence Alignments

LumberJack 7.10

:: DESCRIPTION

LumberJack is a phylogenetic tool intended to serve two purposes: to facilitate sampling treespace to find likely tree topologies quickly, and to map phylogenetic signal onto regions of an alignment in a revealing way.

::DEVELOPER

Lawrence-Dill Plant Informatics and Computation Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 LumberJack

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Aug 12;20(12):1977-9. Epub 2004 Mar 25.
LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference.
Lawrence CJ1, Zmasek CM, Dawe RK, Malmberg RL.

SCFG Structural Entropy 20120907 – Calculate RNA Structural Entropies through Stochastic Context Free Grammars

SCFG Structural Entropy 20120907

:: DESCRIPTION

SCFG Structural Entropy is a software to calculate RNA structural entropies through stochastic context free grammars.

::DEVELOPER

Russell Malmberg Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SCFG Structural Entropy

:: MORE INFORMATION

Citation

J Theor Biol. 2013 Feb 7;318:140-63. doi: 10.1016/j.jtbi.2012.10.023. Epub 2012 Nov 14.
Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA.
Manzourolajdad A1, Wang Y, Shaw TI, Malmberg RL.

TRAMPR 1.0-9 – TRFLP Species Identification

TRAMPR 1.0-9

:: DESCRIPTION

TRAMPR is an R package for matching terminal restriction fragment length polymorphism (TRFLP) profiles between unknown samples and a database of knowns. TRAMPR facilitates analysis of many unknown profiles at once, and provides tools for working directly with electrophoresis output through to generating summaries suitable for community analyses with R’s rich set of statistical functions. TRAMPR also resolves the issues of multiple TRFLP profiles within a species, and shared TRFLP profiles across species.

::DEVELOPER

Rich FitzJohn

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • R package

:: DOWNLOAD

 TRAMPR

:: MORE INFORMATION

mosaic 0.1-1 – Hybrid Zones Analysis

mosaic 0.1-1

:: DESCRIPTION

Mosaic is a software which calculates the ‘mosaicity’ of a one dimensional hybrid zone. This package uses likelihood to fit step-wise models to one dimensional hybrid zone data, and to estimate the ‘mosaicity’ of the hybrid zone.

::DEVELOPER

Rich FitzJohn , Leithen M’Gonigle

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • R package

:: DOWNLOAD

  Mosaic

:: MORE INFORMATION

Citation

Evolution. 2010 Feb 1;64(2):444-55. doi: 10.1111/j.1558-5646.2009.00838.x. Epub 2009 Sep 23.
Assortative mating and spatial structure in hybrid zones.
M’Gonigle LK, FitzJohn RG.

diversitree 0.9-15 – Comparative Phylogenetic Analysis of Diversification in R

diversitree 0.9-15

:: DESCRIPTION

The “diversitree” package includes a number of comparative phylogenetic methods, mostly focussing on analysing diversification and character evolution.

::DEVELOPER

Rich FitzJohn

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • R package

:: DOWNLOAD

 diversitree

:: MORE INFORMATION

Citation

Richard G. FitzJohn
Diversitree: comparative phylogenetic analyses of diversification in R
Issue Methods in Ecology and Evolution Methods in Ecology and Evolution Volume 3, Issue 6, pages 1084–1092, December 2012

FoldUnfold – Prediction of Disordered Regions in Protein Chain

FoldUnfold

:: DESCRIPTION

FoldUnfold is a web server for the prediction of disordered regions in protein chain.

::DEVELOPER

the BioInformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

FoldUnfold: web server for the prediction of disordered regions in protein chain.
Galzitskaya OV, Garbuzynskiy SO, Lobanov MY.
Bioinformatics. 2006 Dec 1;22(23):2948-9. Epub 2006 Oct 4.

IsUnstruct 2.02 – Prediction of Disordered Residues based on the Ising model

IsUnstruct 2.02

:: DESCRIPTION

IsUnstruct is a software of prediction of disordered residues based on the Ising model

::DEVELOPER

the BioInformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 IsUnstruct

:: MORE INFORMATION

Citation

Phys Biol. 2011 Jun;8(3):035004. doi: 10.1088/1478-3975/8/3/035004. Epub 2011 May 13.
The Ising model for prediction of disordered residues from protein sequence alone.
Lobanov MY1, Galzitskaya OV.

H-Protection – Prediction of Residue Status to be protected or unprotected from Hydrogen-deuterium Exchange

H-Protection

:: DESCRIPTION

H-Protection is a web application for prediction of residue status to be protected or unprotected from hydrogen-deuterium exchange in a protein chain

::DEVELOPER

the BioInformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Open Biochem J. 2008;2:77-80. doi: 10.2174/1874091X00802010077. Epub 2008 Jun 3.
Prediction of Residue Status to Be Protected or Not Protected From Hy-drogen Exchange Using Amino Acid Sequence Only.
Nikita V D, Oxana V G.

VIBE 2.0 – Visual Integration for Bayesian Evaluation

VIBE 2.0

:: DESCRIPTION

VIBE software is a visualization tool that allows the user to observe classification accuracies at the class level and evaluate classification accuracies on any subset of available data types based on the posterior probability models defined for the individual and integrated data.

::DEVELOPER

Pacific Northwest National Laboratory (PNNL)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • MatLab 

:: DOWNLOAD

 VIBE

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jan 15;26(2):280-2. doi: 10.1093/bioinformatics/btp639.
VIBE 2.0: visual integration for bayesian evaluation.
Beagley N, Stratton KG, Webb-Robertson BJ.