ScaffoldSeq – Characterization of Directed Evolution Populations

ScaffoldSeq

:: DESCRIPTION

ScaffoldSeq is software designed for the numerous applications – including directed evolution analysis – in which a user generates a population of DNA sequences encoding for partially diverse proteins with related functions and would like to characterize the single site and pairwise amino acid frequencies across the population.

::DEVELOPER

Hackel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Python

:: DOWNLOAD

 ScaffoldSeq

:: MORE INFORMATION

Citation

ScaffoldSeq: Software for characterization of directed evolution populations.
Woldring DR, Holec PV, Hackel BJ.
Proteins. 2016 Mar 28. doi: 10.1002/prot.25040.

SimPhy 1.0.1 – A comprehensive Simulator of Gene Family Evolution

SimPhy 1.0.1

:: DESCRIPTION

SimPhy is a program for the simulation of gene family evolution under incomplete lineage sorting (ILS), gene duplication and loss (GDL), replacing horizontal gene transfer (HGT) and gene conversion (GC).

::DEVELOPER

Phylogenomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsx/Linux

:: DOWNLOAD

 SimPhy

:: MORE INFORMATION

Citation

SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees.
Mallo D, de Oliveira Martins L, Posada D.
Syst Biol. 2015 Nov 1. pii: syv082.

SBEToolbox 1.3.2 – MATLAB Systems Biology & Evolution Toolbox

SBEToolbox 1.3.2

:: DESCRIPTION

SBEToolbox (Systems Biology and Evolution Toolbox) is being developed in MATLAB as a menu-driven GUI software to determine various statistics of the biological network. Some of its features include (but not limited to) algorithms to create random networks (small-world, ring lattice etc..), deduce clusters in the network (MCL, mCode, clusterOne), compute various network topology measures etc…

::DEVELOPER

Cai Laborary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SBEToolbox

:: MORE INFORMATION

Citation

Evol Bioinform Online. 2013 Sep 1;9:355-62. doi: 10.4137/EBO.S12012. eCollection 2013.
SBEToolbox: A Matlab Toolbox for Biological Network Analysis.
Konganti K1, Wang G, Yang E, Cai JJ.

SGWE 7.3.5 / CoalEvol 7.3.5 – Simulation of Genome-Wide Evolution

SGWE 7.3.5 / CoalEvol 7.3.5

:: DESCRIPTION

SGWE consists of a GUI and a pipeline of scripts for the simulation of genome/proteome-wide evolution under heterogeneous substitution models and a variety of evolutionary scenarios.

CoalEvol generates samples of nucleotide, codon and amino acid sequences, contemporaneous or not, from populations evolved under a neutral coalescent model with a variety of evolutionary scenarios such as recombination (including recombination hotspots and intracodon recombination), migration, demographics and species/population trees

::DEVELOPER

Dr. MIGUEL ARENAS

:: SCREENSHOTS

N/a

:: REQUIREMENTS

:: DOWNLOAD

  SGWE , CoalEvol

:: MORE INFORMATION

Citation

Mol Biol Evol. 2014 May;31(5):1295-301. doi: 10.1093/molbev/msu078. Epub 2014 Feb 19.
Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories.
Arenas M1, Posada D.

windex 1.0 – Analysing Convergent Evolution using the Wheatsheaf index

windex 1.0

:: DESCRIPTION

windex is a package developed for the R statistical environment to provide novel tools for the analysis of convergent evolution.

::DEVELOPER

windex team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 windex

:: MORE INFORMATION

Citation

Evol Bioinform Online. 2015 Feb 12;11:11-4. doi: 10.4137/EBO.S20968. eCollection 2015.
windex: Analyzing Convergent Evolution Using the Wheatsheaf Index in R.
Arbuckle K, Minter A.

APE 3.3 – Analysis of Phylogenetics and Evolution

APE 3.3

:: DESCRIPTION

APE (Analysis of Phylogenetics and Evolution) is a package for the analysis of phylogenetics and evolution.APE provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading nucleotide sequences, and several tools such as Mantel’s test, computation of minimum spanning tree, generalized skyline plots, estimation of absolute evolutionary rates and clock-like trees using mean path lengths, non-parametric rate smoothing and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, and ME methods.

::DEVELOPER

APE Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 APE

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Jun 1;28(11):1536-7. doi: 10.1093/bioinformatics/bts184. Epub 2012 Apr 11.
ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R.
Popescu AA1, Huber KT, Paradis E.

Paradis E., Claude J. & Strimmer K. 2004.
APE: analyses of phylogenetics and evolution in R language.
Bioinformatics 20: 289–290.

Crann 1.04 – Detect Adaptive Evolution in Protein-coding DNA Sequences

Crann 1.04

:: DESCRIPTION

Crann (pronounced ‘crown’) is the Irish word for ‘tree’.Crann has been developed in order to provide fast heuristic methods of detecting adaptive evolution in protein-coding genes. It is important that the user understands the advantages and limitations of these methods. It is also important for the user to know that the software is designed to perform a number of different tasks, however the interpretation of the results is left entirely to the user.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Crann

:: MORE INFORMATION

Citation:

Creevey, C. and J. O. McInerney (2003).
CRANN: Detecting adaptive evolution in protein-coding DNA sequences
Bioinformatics (2003) 19: 1726.

nextflu – Real-time Tracking of Influenza Evolution

nextflu

:: DESCRIPTION

nextflu is designed to perform near real-time tracking of influenza virus evolution.

::DEVELOPER

Trevor Bedford and Richard Neher.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web server

:: DOWNLOAD

 nextflu

:: MORE INFORMATION

Citation:

nextflu: real-time tracking of seasonal influenza virus evolution in humans.
Neher RA, Bedford T.
Bioinformatics. 2015 Jun 26. pii: btv381.

REX – Region Evolution eXplorer

REX

:: DESCRIPTION

REX is a web-based system for exploring the evolution of ontology parts (regions).

::DEVELOPER

Interdisciplinary Centre for Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Region Evolution eXplorer – A tool for discovering evolution trends in ontology regions.
Christen V, Hartung M, Groß A.
J Biomed Semantics. 2015 Jun 1;6:26. doi: 10.1186/s13326-015-0020-6. eCollection 2015.

UniAlign – Protein Pairwise Structure Alignment with Evolution and Sequence Information

UniAlign

:: DESCRIPTION

UniAlign is a new protein pairwise structure alignment algorithm that incorporates additional evolutionary information captured in the form of sequence similarity, sequence profiles, and residue conservation.

::DEVELOPER

Sacan Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

 

:: MORE INFORMATION

Citation

UniAlign: Protein Structure Alignment Meets Evolution.
Zhao C, Sacan A.
Bioinformatics. 2015 Jun 9. pii: btv354.