DupliPHY 2.0 / DupliPHY-ML 1.2 – Determine the Evolutionary Histories of Gene Families

DupliPHY 2.0 / DupliPHY-ML 1.2

:: DESCRIPTION

DupliPHY is a software tool to determine the evolutionary histories of gene families over a phylogenetic tree. Given a set of gene family sizes and a phylogenetic tree DupliPHY will calculate the ancestral family sizes at each internal node within the tree.

DupliPHY-ML is a software tool to determine the evolutionary histories of gene families using maximum likelihood.Given a set of gene family sizes and a phylogenetic tree DupliPHY-ML will calculate the ancestral family sizes at each internal node within the tree, the average number of events per branch, estimates of rates of birth-death and an evolutionary rate for each family.

::DEVELOPER

LOVELL LAB

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux/ Windows/ MacOsX
Java

:: DOWNLOAD

DupliPHY / DupliPHY-ML

:: MORE INFORMATION

Citation:

DupliPHY-Web: A web server for DupliPHY and DupliPHY-ML.
Ames RM, Lovell SC.
Bioinformatics. 2014 Oct 7. pii: btu645.

Ames RM, Money D, Ghatge VP, Whelan S and Lovell SC.
Determining the evolutionary history of gene families.
Bioinformatics (2012) 28(1): 48-55.

Arboretum – Reconstruction and analysis of Evolutionary History of Condition-specific Transcriptional Modules

Arboretum

:: DESCRIPTION

Arboretum is a novel scalable computational algorithm that integrates expression data from multiple species with species and gene phylogenies to infer modules of coexpressed genes in extant species and their evolutionary histories.

::DEVELOPER

Roy Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Arboretum

:: MORE INFORMATION

Citation

Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules.
Roy S, Wapinski I, Pfiffner J, French C, Socha A, Konieczka J, Habib N, Kellis M, Thompson D, Regev A.
Genome Res. 2013 Jun;23(6):1039-50. doi: 10.1101/gr.146233.112.

CHROnicle 201503 – Reconstruction of the complete Evolutionary History of Genomes

CHROnicle 201503

:: DESCRIPTION

CHROnicle is a package dedicated to the reconstruction of the complete evolutionary history of genomes. It is based on the analysis of the marks accumulated over evolutionary time left in the genomes by chromosomal rearrangements. CHROnicle is composed of four different programs: SynChro, PhyChro, ReChro and AnChro.

::DEVELOPER

Laboratory of Computational and Quantitative Biology(LCQB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX

:: DOWNLOAD

CHROnicle

:: MORE INFORMATION

Citation

PLoS One. 2014 Mar 20;9(3):e92621. doi: 10.1371/journal.pone.0092621. eCollection 2014.
SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.
Drillon G1, Carbone A2, Fischer G

HiDe 20120609 – Infer Highways of Horizontal Gene Transfer in the Evolutionary History of a set of Species

HiDe 20120609

:: DESCRIPTION

HiDe (short for Highway Detection) is a software package for inferring highways of horizontal gene transfer in the evolutionary history of a set of species. HiDe takes as input a collection of unrooted gene trees along with a rooted species tree.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

Windows/Linux

:: DOWNLOAD

HiDe

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Mar 1;29(5):571-9. doi: 10.1093/bioinformatics/btt021. Epub 2013 Jan 17.
Systematic inference of highways of horizontal gene transfer in prokaryotes.
Bansal MS, Banay G, Harlow TJ, Gogarten JP, Shamir R.

DILTAG – Inferring the Evolutionary History of Gene Clusters from Phylogenetic and Gene Order Data

DILTAG

:: DESCRIPTION

DILTAG is an algorithm allowing to infer a set of optimal evolutionary histories for a gene cluster in a single species, according to a general cost model involving variable length duplications (in tandem or inverted), deletions, and inversions.

::DEVELOPER

NADIA EL-MABROUK

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

M. Lajoie, D. Bertrand and N. El-Mabrouk.
Inferring the Evolutionary History of Gene Clusters from Phylogenetic and Gene Order Data.
Mol Biol Evol. 2010 Apr;27(4):761-72. doi: 10.1093/molbev/msp271