Tag: Gene Family

DLTCount – Counting and Sampling Gene Family Histories

DLTCount

:: DESCRIPTION

DLTCount : Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DLTCount

:: MORE INFORMATION

Citation

Chauve C, Ponty Y, Wallner M.
Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models.
J Math Biol. 2020 Apr;80(5):1353-1388. doi: 10.1007/s00285-019-01465-x. Epub 2020 Feb 15. PMID: 32060618; PMCID: PMC7052048.

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.

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.

MetaPASSAGE – Automated Simulations and Analysis of Gene Families

MetaPASSAGE

:: DESCRIPTION

MetaPASSAGE, a software pipeline to generate in silico bacterial communities, simulates a sample of shotgun reads from a gene family represented in the community, orient or translate reads, and produce a profile-based alignment of the reads from which a gene-family phylogenetic tree can be built.

::DEVELOPER

Pollard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl

:: DOWNLOAD

 MetaPASSAGE

:: MORE INFORMATION

Citation

BMC Genomics. 2013 Jun 22;14:419. doi: 10.1186/1471-2164-14-419.
Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis.
Riesenfeld SJ, Pollard KS.

GFam 1.4 – Gene Family Annotation & Maintenance

GFam 1.4

:: DESCRIPTION

GFam is a command-line tool for automatic annotation of gene families. GFam offers a framework for complete genome initiatives and model organism resources to build domain-based gene families, derive meaningful functional labels and maintain family annotation across genome releases seamlessly. Our approach achieves a unified system for grouping proteins based on evolutionary and functional relationships.

::DEVELOPER

Paccanaro Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 GFam

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Oct;40(19):e152. doi: 10.1093/nar/gks631. Epub 2012 Jul 11.
GFam: a platform for automatic annotation of gene families.
Sasidharan R1, Nepusz T, Swarbreck D, Huala E, Paccanaro A.

BEGFE 1.1 – Bayesian Estimation of Gene Family Evolution

BEGFE 1.1

:: DESCRIPTION

BEGFE implements a Markov Chain Monte Carlo algorithm to estimate the posterior probability distribution of the birth and death rate parameters and the numbers of gene copies at the internodes of the phylogenetic tree. In addition, BEGFE can simulate gene family data under the birth and death model.

::DEVELOPER

Phylogenetics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/ Windows

:: DOWNLOAD

BEGFE

:: MORE INFORMATION

Citation

Liu, L., L. Yu, V. Kalavacharla, Z. Liu.
A Bayesian model for gene family evolution.
BMC Bioinformatics. 2011, 12:426

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.

BranchClust 1.01 – A Phylogenetic Algorithm for Selecting Gene Families

BranchClust 1.01

:: DESCRIPTION

BranchClust is an algorithm for the automated selection of orthologous genes that recognizes orthologous genes from different species in a phylogenetic tree for any number of taxa. The algorithm is capable of distinguishing complete (containing all taxa) and incomplete (not containing all taxa) families and recognizes in- and out-paralogs.

::DEVELOPER

Gogarten Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • Bioperl

:: DOWNLOAD

  BranchClust

:: MORE INFORMATION

Citation

Maria S Poptsova and J Peter Gogarten
BranchClust: a phylogenetic algorithm for selecting gene families
BMC Bioinformatics 2007, 8:120