Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network
Open Access
- 14 July 2006
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 22 (18) , 2313-2314
- https://doi.org/10.1093/bioinformatics/btl387
Abstract
Summary:Serial NetEvolve is a flexible simulation program that generates DNA sequences evolved along a tree or recombinant network. It offers a user-friendly Windows graphical interface and a Windows or Linux simulator with a diverse selection of parameters to control the evolutionary model. Serial NetEvolve is a modification of the Treevolve program with the following additional features: simulation of serially-sampled data, the choice of either a clock-like or a variable rate model of sequence evolution, sampling from the internal nodes and the output of the randomly generated tree or network in our newly proposed NeTwick format. Availability: From website Contacts:giri@cis.fiu.edu Supplementary information: Manual and examples available fromKeywords
This publication has 13 references indexed in Scilit:
- Properties of a neutral allele model with intragenic recombinationPublished by Elsevier ,2004
- Serial SimCoal: A population genetics model for data from multiple populations and points in timeBioinformatics, 2004
- RDP2: recombination detection and analysis from sequence alignmentsBioinformatics, 2004
- The causes and consequences of HIV evolutionNature Reviews Genetics, 2004
- Evolutionary Indicators of Human Immunodeficiency Virus Type 1 Reservoirs and CompartmentsJournal of Virology, 2003
- PAL: an object-oriented programming library for molecular evolution and phylogeneticsBioinformatics, 2001
- Reconstructing Genealogies of Serial Samples Under the Assumption of a Molecular Clock Using Serial-Sample UPGMAMolecular Biology and Evolution, 2000
- Population Dynamics of HIV-1 Inferred From Gene SequencesGenetics, 1999
- The coalescentStochastic Processes and their Applications, 1982
- Comparison of phylogenetic treesMathematical Biosciences, 1981