Tag: Evolution

VarEff 1.2 – Detecting the Evolution of the Coalescent Effective Population Size

VarEff 1.2

:: DESCRIPTION

VarEff estimates the effective sizes from actual to ancestral time with a coalescent approach. It works on steps of constant size to resolve the probabilities by an approximation of maximum likelihood from a Bayesian posterior distribution.

::DEVELOPER

VarEff Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R pacakge

:: DOWNLOAD

 VarEff

:: MORE INFORMATION

Citation

Chevalet C & Nikolic N. 2010.
Distribution of coalescent times and distances between microsatellite alleles with changing effective population size.
Theoretical Population Biology. Volume 77, Issue 3: 152-163

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.

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.

nextflu 1.0 – Real-time Tracking of Influenza Evolution

nextflu 1.0

:: DESCRIPTION

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

::DEVELOPER

bedford lab

:: 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.

APE 5.5 – Analysis of Phylogenetics and Evolution

APE 5.5

:: 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.

windex 2.0.2 – Analysing Convergent Evolution using the Wheatsheaf index

windex 2.0.2

:: 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.

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.

SimPhy 1.0.2 – A comprehensive Simulator of Gene Family Evolution

SimPhy 1.0.2

:: 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.

MySSP 1.0.3.5 – Simulation of DNA Sequence Evolution across a Phylogenetic Tree

MySSP 1.0.3.5

:: DESCRIPTION

MySSP is a program for the simulation of DNA sequence evolution across a phylogenetic tree

::DEVELOPER

Michael S. Rosenberg’s Laboratory

:: SCREENSHOTS

MySSP

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MySSP

:: MORE INFORMATION

Citation

Rosenberg, M.S. (2005)
MySSP: Non-stationary evolutionary sequence simulation, including indels.
Evolutionary Bioinformatics Online 1:81–83

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.