dnet 1.1.5 – Integrative Analysis of Omics data in terms of Network, Evolution and Ontology

dnet 1.1.5

:: DESCRIPTION

dnet is an open-source R package for omics data integrative analysis in terms of network, evolution and ontology

::DEVELOPER

Dr. Hai Fang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 dnet

:: MORE INFORMATION

Citation:

Genome Med. 2014 Aug 26;6(8):64. doi: 10.1186/s13073-014-0064-8.
The ‘dnet’ approach promotes emerging research on cancer patient survival.
Fang H, Gough J

SPECTRE 1.1.5 – Suite of Phylogenetic tools for Reticulate Evolution

SPECTRE 1.1.5

:: DESCRIPTION

SPECTRE provides several new implementations of pre-published algorithms to construct phylogenetic trees and networks (more precisely split networks), along with an interactive graphical interface for visualizing planar split networks.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SPECTRE 

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Mar 15;34(6):1056-1057. doi: 10.1093/bioinformatics/btx740.
SPECTRE: a suite of phylogenetic tools for reticulate evolution.
Bastkowski S, Mapleson D, Spillner A, Wu T, Balvociute M, Moulton V.

PGEToolbox 3.0 – Matlab Toolbox for Population Genetics and Evolution

PGEToolbox 3.0

:: DESCRIPTION

PGEToolbox is a Matlab-based software package for analysis of polymorphism and divergence data for population genetics and evolution. It estimates several basic statistics of DNA sequence variation and carries out statistical tests of selective neutrality under the infinite alleles model, such as Tajima’s D test, Fu & Li’s tests and Fay & Wu’s H test. The significance of tests is determined from the distribution of the statistics obtained by coalescent simulation. The toolbox performs McDonald-Kreitman test (and several extensions). PGEToolbox also contains functions for handling SNP (Single Nucleotide Polymorphism) genotype data. PGEToolbox is open-sourced, can be easily extended or tailored for specific tasks, and scaled up for large data sets.

::DEVELOPER

Cai Laborary

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  PGEToolbox

:: MORE INFORMATION

Citation:

Cai JJ (2008)
PGEToolbox: A Matlab toolbox for population genetics and evolution
Journal of Heredity Jul-Aug;99(4):438-40. doi:10.1093/jhered/esm127

SDSE 2.0 – Simulation of DNA Sequence Evolution

SDSE 2.0

:: DESCRIPTION

SDSE is an  algorithm  to  simulate  DNA  sequence  evolution  under  a  general  stochastic  model,  including  as  particular  cases  all  the  previously  used  schemes  of  nucleotide  substitution

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

SDSE

:: REQUIREMENTS

  • DOS

:: DOWNLOAD

 SDSE

:: MORE INFORMATION

Citation:

Comput Appl Biosci. 1989 Feb;5(1):47-50.
SDSE: a software package to simulate the evolution of a pair of DNA sequences.
Oliver JL, Marín A, Medina JR.

nhPhyML – Compute Phylogenetic Trees under non Homogeneous model of DNA sequence Evolution

nhPhyML

:: DESCRIPTION

nhPhyML is a program built to compute phylogenetic trees under the non stationary, non homogeneous model of DNA sequence evolution of Galtier and Gouy (1998).

::DEVELOPER

Bastien Boussau

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX

:: DOWNLOAD

  nhPhyML

:: MORE INFORMATION

Citation

Efficient likelihood computations with nonreversible models of evolution.
Boussau B, Gouy M.
Syst Biol. 2006 Oct;55(5):756-68.

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

SANTA-SIM 1.0 – Simulate the Evolution of Population of Gene Sequences Forwards through Time

SANTA-SIM 1.0

:: DESCRIPTION

SANTA-SIM is a forward-time simulator for gene sequences modeling a variety of mutation and selection processes.

::DEVELOPER

SANTA-SIM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

SANTA-SIM

:: MORE INFORMATION

Citation:

SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination.
Jariani A, Warth C, Deforche K, Libin P, Drummond AJ, Rambaut A, Matsen Iv FA, Theys K.
Virus Evol. 2019 Mar 8;5(1):vez003. doi: 10.1093/ve/vez003.

Seq-Gen 1.3.4 – Simulate the Evolution of Sequences along a Phylogeny

Seq-Gen 1.3.4

:: DESCRIPTION

Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Seq-Gen

:: MORE INFORMATION

Citation

Comput Appl Biosci. 1997 Jun;13(3):235-8.
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees.
Rambaut A1, Grassly NC.

PhyloWGS 1.0-rc2 – Inferring Subclonal Composition and Evolution from Whole-genome Sequencing data

PhyloWGS 1.0-rc2

:: DESCRIPTION

PhyloWGS can be applied to whole-genome sequencing data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations and population frequencies of structural variations.

::DEVELOPER

Morris Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • Python

:: DOWNLOAD

  PhyloWGS

:: MORE INFORMATION

Citation

Genome Biol. 2015 Feb 13;16(1):35. doi: 10.1186/s13059-015-0602-8.
PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors.
Deshwar AG, Vembu S, Yung CK, Jang GH, Stein L, Morris Q.

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.