Tag: Sequence Evolution

Dawg 1.2 – Simulating Sequence Evolution

Dawg 1.2

:: DESCRIPTION

Dawg (DNA Assembly with Gaps) is an application designed to simulate the evolution of recombinant DNA sequences in continuous time based on the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation.

::DEVELOPER

Reed A. Cartwright

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 Dawg

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Nov 1;21 Suppl 3:iii31-8.
DNA assembly with gaps (Dawg): simulating sequence evolution.
Cartwright RA

iCataly-PseAAC – Identification of Enzymes Catalytic sites using Sequence Evolution information

iCataly-PseAAC

:: DESCRIPTION

The web-server iCatalytic-PseAAC is a web server that could predict methylation sites in proteins. With the assistance of FKNN, the highlight of iCatalytic-PseAAC is to employ amino acid sequence features extracted by incorporating the sequence evolution information into PseAAC via a grey system model (Grey-PSSM).

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Membr Biol. 2015 Jun 16.
iCataly-PseAAC: Identification of Enzymes Catalytic Sites Using Sequence Evolution Information with Grey Model GM (2,1).
Xiao X1, Hui MJ, Liu Z, Qiu WR.

traitRate 201612 – Detection of Trait-dependent Shifts in the Rate of Sequence Evolution

traitRate 201612

:: DESCRIPTION

traitRate is a program for the detection of trait-dependent shifts in the rate of sequence evolution.

::DEVELOPER

Mayrose Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

  traitRate

:: MORE INFORMATION

Citation

Mayrose I and Otto SP. 2011.
A Likelihood Method for Detecting Trait-Dependent Shifts in the Rate of Molecular Evolution.
Mol Biol Evol. 28:781-791.

Alfacinha – Simulation of Sequence Evolution with Neighbouring-site Dependencies

Alfacinha

:: DESCRIPTION

alfacinha is a source-package of object-oriented Python modules for sequence evolution allowing for neighbor-dependent substitutions under GPL license.This package is aimed at simulating the evolution of sequences along phylogenetic trees. It provides several modules to store and manipulate evolutionary models, to store and evolve a sequence, and store and manipulate evolutionary trees

::DEVELOPER

Leonor Palmeira.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Alfacinha Source Code

:: MORE INFORMATION

 

 

ROSE 1.3.1 – Random-model Of Sequence Evolution

ROSE 1.3.1

:: DESCRIPTION

Rose (Random-model Of Sequence Evolution) implements a new probabilistic model of the evolution of RNA-, DNA-, or protein-like sequences. Guided by an evolutionary tree, a family of related sequences is created from a common ancestor sequence by insertion, deletion and substitution of characters. During this artificial evolutionary process, the `true’ history is logged and the `correct’ multiple sequence alignment is created simultaneously. The model also allows for varying rates of mutation within the sequences, making it possible to establish so-called sequence motifs.

::DEVELOPER

Jens Stoye – Folker Meyer – Dirk Evers

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ROSE

:: MORE INFORMATION

Citation

Rose: generating sequence families
J. Stoye, D. Evers, F. Meyer
in: Bioinformatics – (formerly CABIOS), Volume 14, Issue 2, March 1998, pp. 157-163, OUP Press

PhyloSim 3.0.5 – Monte Carlo Simulation of Sequence Evolution

PhyloSim 3.0.5

:: DESCRIPTION

PhyloSim is an extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PhyloSim

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 Apr 19;12:104.
PhyloSim – Monte Carlo simulation of sequence evolution in the R statistical computing environment.
Sipos B, Massingham T, Jordan GE, Goldman N.

BEAGLE 3.1.2 – Evaluating the Likelihood of Sequence Evolution on Trees

BEAGLE 3.1.2

:: DESCRIPTION

BEAGLE-lib (Broad-platform Evolutionary Analysis General Likelihood Evaluator) is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.

::DEVELOPER

BEAGLE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 BEAGLE 

:: MORE INFORMATION

Citation

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics.
Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA.
Syst Biol. 2019 Nov 1;68(6):1052-1061. doi: 10.1093/sysbio/syz020.

Syst Biol. 2012 Jan;61(1):170-3. doi: 10.1093/sysbio/syr100.
BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.
Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA.

SISSI 1.0 – Simulating Sequence Evolution with Site-Specific Interactions

SISSI 1.0

:: DESCRIPTION

SISSI (Simulating Sequence Evolution with Site-Specific Interactions)  is a software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows /MacOsX

:: DOWNLOAD

 SISSI

:: MORE INFORMATION

Citation:

Tanja Gesell and Arndt von Haeseler:
In silico sequence evolution with site-specific interactions along phylogenetic trees, Phylogenetic Trees.
Bioinformatics, 22:716-722, 2006.

REvolver 1.0 – Modeling Sequence Evolution under Domain Constraints

REvolver 1.0

:: DESCRIPTION

REvolver is a program to simulate protein sequence evolution. REvolver automatically integrates domain information described by a profile Hidden Markov Model (pHMM) into the simulation.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows /MacOsX
  • Java

:: DOWNLOAD

 REvolver

:: MORE INFORMATION

Citation:

Tina Koestler, Arndt von Haeseler, and Ingo Ebersberger (2012)
REvolver: Modeling sequence evolution under domain constraints.
Mol Biol Evol (2012)doi: 10.1093/molbev/mss078