DAMBE 5.3.48 – Sequence Data Analysis in Molecular Biology and Evolution

DAMBE 5.3.48

:: DESCRIPTION

DAMBE (data analysis in molecular biology and evolution) is an integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data.

::DEVELOPER

Dr. Xuhua Xia

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / Mac OsX

:: DOWNLOAD

DAMBE

:: MORE INFORMATION

Citation:

Xia, X. 2013.
DAMBE5: A comprehensive software package for data analysis in molecular biology and evolution.
Molecular Biology and Evolution 30:1720-1728

Xia, X., and Xie. Z., 2001
DAMBE: Data analysis in molecular biology and evolution.
Journal of Heredity 92:371-373.

ECR Browser – Interactive Browser of Genome Conservation and Evolution

ECR Browser

:: DESCRIPTION

The ECR Browser is a dynamic graphical interface that allows users to visualize and analyze Evolutionary Conserved Regions (ECRs) in genomes of sequenced species.

::DEVELOPER

Ivan Ovcharenko Research Group

:: SCREENSHOTS

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.
Ovcharenko I, Nobrega MA, Loots GG, Stubbs L.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W280-6.

ProtTest 3.3 – Selection of Best-fit Models of Protein Evolution

ProtTest 3.3

:: DESCRIPTION

ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand. ProtTest makes this selection by finding the model in the candidate list with the smallest Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT). At the same time, ProtTest obtains model-averaged estimates of different parameters (including a model-averaged phylogenetic tree) and calculates their importance(Posada and Buckley 2004). ProtTest differs from its nucleotide analog jModeltest (Posada 2008) in that it does not include likelihood ratio tests, as not all models included in ProtTest are nested.

::DEVELOPER

Phylogenomics Group at the University of Vigo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX / Linux
Java
PhyML

:: DOWNLOAD

ProtTest

:: MORE INFORMATION

Citation:

Darriba D, Taboada GL, Doallo R, Posada D.
ProtTest 3: fast selection of best-fit models of protein evolution.
Bioinformatics (2011)doi: 10.1093/bioinformatics/btr088

Lagrange 20130526 – Likelihood Analysis of Geographic Range Evolution

Lagrange 20130526

:: DESCRIPTION

Lagrange is a Python package implementing likelihood models for geographic range evolution on phylogenetic trees, with methods for inferring rates of dispersal and local extinction and ancestral ranges.

Lagrange Online Version

::DEVELOPER

STEPHEN A. SMITH , Rick Ree

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX
Python

:: DOWNLOAD

Lagrange

:: MORE INFORMATION

Citation

Ree, R H and S A Smith. 2008.
Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis.
Systematic Biology 57(1):4-14.

SimCopy 0.2 – Simulate the Evolution of Copy Number Profiles along a Tree

SimCopy 0.2

:: DESCRIPTION

SimCopy is an R package simulating the evolution of copy number profiles along a tree. It relies on the PhyloSim package for performing the simulations by encoding the genomic regions as sites in sequences and using modified processes acting on them.

::DEVELOPER

Botond Sipos

:: REQUIREMENTS

Linux / Windows / MacOsX
PhyloSim
r package

:: DOWNLOAD

SimCopy

:: MORE INFORMATION

EvoDots 1.1 – Explore the Mechanism of Evolution

EvoDots 1.1

:: DESCRIPTION

EvoDots lets the user explore the mechanism of evolution. The program creates a population of dots. The user is a predator. As the dots run around the screen, the user eats them by clicking on them with the mouse. After the user has eaten some of the dots, the survivors will reproduce. The population may or may note evolve, depending on the properties of the dots.

::DEVELOPER

Jon C. Herron

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX / Windows

:: DOWNLOAD

EvoDots

:: MORE INFORMATION

AlleleA1 2.0 – Simulate Evolution at a single locus in an ideal Population of Imaginary Organisms

AlleleA1 2.0

:: DESCRIPTION

AlleleA1 simulates evolution at a single locus in an ideal population of imaginary organisms. The locus of interest has 2 alleles: A1 and A2. The user enters values for parameters controlling selection, mutation, migration, genetic drift, and inbreeding. As the simulation runs, the software plots a graph showing the frequency of allele A1 over time.

::DEVELOPER

Jon C. Herron

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX / Windows

:: DOWNLOAD

AlleleA1

:: MORE INFORMATION

Is it Chance 1.0 – Is Evolution by Natural Selection “just chance?”

Is it Chance 1.0

:: DESCRIPTION

Is It Chance is a very simple little program that demonstrates the power of natural selection to accumulate favorable variations is anything but “mere chance.”.Is It Chance pits chance and selection against each other in a race to match a string of random letters to a sentence typed in by the user, and reveals clearly the difference between natural selection and “mere chance.”

::DEVELOPER

The Queller/Strassmann Research Group at Washington University in St. Louis

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac

:: DOWNLOAD

Is It Chance

:: MORE INFORMATION

RANGER-DTL 1.0 – Rapid ANalysis of Gene family Evolution using Reconciliation-DTL

RANGER-DTL 1.0

:: DESCRIPTION

RANGER-DTL is a software package for inferring gene family evolution by speciation, gene duplication, horizontal gene transfer, and gene loss. The software takes as input a gene tree (rooted or unrooted) and a rooted species tree and reconciles the two by postulating speciation, duplication, transfer, and loss events. RANGER-DTL implements efficient algorithms that can efficiently analyze trees with even thousands of taxa, and can handle both undated and dated species trees (i.e., both cladograms and chronograms).

::DEVELOPER

Mukul Bansal @ MIT Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX/ Windows

:: DOWNLOAD

RANGER-DTL

:: MORE INFORMATION

Citation

Efficient Algorithms for the Reconciliation Problem with Gene Duplication, Horizontal Transfer, and Loss
Mukul S. Bansal, Eric J. Alm, Manolis Kellis.
ISMB 2012; Bioinformatics 28: i283-i291, 2012.

PLEX 0.95 – Phylogenetics, Likelihood, Evolution, and CompleXity

PLEX 0.95

:: DESCRIPTION

The PLEX package is designed to perform rapid likelihood analysis on large phylogenies using partial sampling of substitution histories.

::DEVELOPER

Pollock Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Perl
R package

:: DOWNLOAD

PLEX

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2989-90. doi: 10.1093/bioinformatics/bts555. Epub 2012 Sep 12.
Phylogenetics, likelihood, evolution and complexity.
de Koning AP, Gu W, Castoe TA, Pollock DD.