BitPhylogeny 0.99 – Reconstruct Intra-tumor Evolutionary Pathways

BitPhylogeny 0.99

:: DESCRIPTION

BitPhylogeny is a probabilistic framework to reconstruct intra-tumor evolutionary pathways.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python
  • R

:: DOWNLOAD

 BitPhylogeny

:: MORE INFORMATION

Citation

Genome Biol. 2015 Feb 13;16:36. doi: 10.1186/s13059-015-0592-6.
BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies.
Yuan K, Sakoparnig T, Markowetz F, Beerenwinkel N.

Galaxy 19.09 – Evolutionary and Data Processing Module Development

Galaxy 19.09

:: DESCRIPTION

Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.

::DEVELOPER

Galaxy Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux
  • Python

:: DOWNLOAD

 Galaxy

:: MORE INFORMATION

Citation

Genome Res. 2009 Nov;19(11):2144-53. Epub 2009 Oct 9.
Windshield splatter analysis with the Galaxy metagenomic pipeline.
Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A; Galaxy Team.

MEGA 10.0 – Molecular Evolutionary Genetics Analysis

MEGA 10.0

:: DESCRIPTION

MEGA (Molecular Evolutionary Genetics Analysis)is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.

::DEVELOPER

MEGA Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

MEGA

:: MORE INFORMATION

Citation

Mol Biol Evol. 2013 Dec;30(12):2725-9. doi: 10.1093/molbev/mst197. Epub 2013 Oct 16.
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011)
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods.
Molecular Biology and Evolution (2011)doi: 10.1093/molbev/msr121 First published online: May 4, 2011

PhyloHMM v2 – Proteome-wide Discovery of Evolutionary Conserved Sequences in Disordered regions

PhyloHMM v2

:: DESCRIPTION

PhyloHMM (phylogenetic hidden Markov model) is a website with data, software and supporting materials for conserved sequences in disordered regions

::DEVELOPER

Alan Moses’ Computational Biology Lab,University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 phylo_HMM

:: MORE INFORMATION

Citation

A. N. Nguyen Ba, B. J. Yeh, D. van Dyk, A. R. Davidson, B. J. Andrews, E. L. Weiss, A. M. Moses,
Proteome-wide discovery of evolutionary conserved sequences in disordered regions.
Sci. Signal. (2012) 5, rs1.

EPPIC 2.1.2 – Evolutionary Protein-Protein Interface Classifier

EPPIC 2.1.2

:: DESCRIPTION

EPPIC aims at classifying the interfaces present in protein crystal structures in order to determine whether they are biologically relevant or not.

::DEVELOPER

EPPIC team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux / MacOsX
  • Java

:: DOWNLOAD

 EPPIC

:: MORE INFORMATION

Citation

Protein interface classification by evolutionary analysis.
Duarte JM, Srebniak A, Schärer MA, Capitani G.
BMC Bioinformatics. 2012 Dec 22;13:334. doi: 10.1186/1471-2105-13-334.

ERD – Evolutionary RNA Designer

ERD

:: DESCRIPTION

ERD designs sequences that fold into a given target RNA secondary structure, i.e. whose minimum free energy (MFE) structure is the target structure.

::DEVELOPER

ERD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ERD

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 1;30(9):1250-8. doi: 10.1093/bioinformatics/btu001. Epub 2014 Jan 8.
Evolutionary solution for the RNA design problem.
Esmaili-Taheri A1, Ganjtabesh M, Mohammad-Noori M.

OpenMEE beta – Ecological and Evolutionary Meta-analysis

OpenMEE beta

:: DESCRIPTION

OpenMEE is a user-friendly, open-source program for carrying out meta-analysis in ecology and evolution. The aim is to make newly developed statistical approaches easily accessible to all. These statistics include: multi-factor meta-analysis, meta-regression, and phylogenetic meta-analysis.

::DEVELOPER

The Center for Evidence-Based Medicine (CEBM) @ Brown

:: SCREENSHOTS

OpenMEE

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

 OpenMEE

:: MORE INFORMATION