MEGA 11 – Molecular Evolutionary Genetics Analysis

MEGA 11

:: 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

EDCNN -Identification of Genome-Wide RNA-binding Proteins Using Evolutionary Deep Convolutional Neural Network

EDCNN

:: DESCRIPTION

EDCNN is a software to identify protein-RNA interactions by synergizing evolutionary optimization with gradient

::DEVELOPER

EDCNN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
Python

:: DOWNLOAD

EDCNN

:: MORE INFORMATION

Citation

Wang Y, Yang Y, Ma Z, Wong KC, Li X.
EDCNN: Identification of Genome-Wide RNA-binding Proteins Using Evolutionary Deep Convolutional Neural Network.
Bioinformatics. 2021 Oct 25:btab739. doi: 10.1093/bioinformatics/btab739. Epub ahead of print. PMID: 34694393.

OpenMEE 2016 – Ecological and Evolutionary Meta-analysis

OpenMEE 2016

:: 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

:: REQUIREMENTS

Windows / MacOsX

:: DOWNLOAD

OpenMEE

:: MORE INFORMATION

GFICLEE 1.0 – Gene Function Inferred by Common Loss Evolutionary Events

GFICLEE 1.0

:: DESCRIPTION

GFICLEE is a program for predicting the new members in biological pathway or biological complex. It is based on the common loss events in gene evolution.

::DEVELOPER

Yang Fang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows / MacOS
Java

:: DOWNLOAD

GFICLEE

:: MORE INFORMATION

Citation

Fang Y, Li M, Li X, Yang Y.
GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level.
BMC Genomics. 2021 Oct 29;22(1):774. doi: 10.1186/s12864-021-08070-7. PMID: 34715785; PMCID: PMC8557005.

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.

EPPIC 3.3.3 – Evolutionary Protein-Protein Interface Classifier

EPPIC 3.3.3

:: 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.

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.

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.