Software
SGWE - Genome evolution under complex evolutionary scenarios
CoalEvol - DNA, codon and protein evolution with complex recombination, migration, demographics and species trees. It improves Recodon and NetRecodon
ProteinEvolver - Protein evolution accounting for structural protein constrains
NetRecodon - DNA and codon evolution with recombination, migration and demographics
Recodon - DNA and codon evolution with recombination, migration and demographics
Splatche - Simulation of genetic data (DNA, SNP, STR) under spatially-explicit evolutionary scenarios. In collaboration with Mathias Currat, Claudio Quilodran, Laurent Excoffier and Nicolas Ray (main developers)
ProtASR - Ancestral sequence reconstruction of proteins accounting forprotein folding stability
CodABC - Coestimation of recombination, substitution and molecular adaptation (dN/dS) rates by approximate Bayesian computation
ProteinEvolverABC - Coestimation of recombination and substitution rates in multiple alignments of protein sequences using approximate Bayesian computation
NetTest - Mathematical characterization of phylogenetic networks
SIMULATION OF GENETIC DATA
SGWE. Simulation of genome/proteome-wide evolution under heterogeneous substitution models and a variety of evolutionary scenarios.
Current version is 7.3.5
© 2012-2014 Miguel Arenas & David Posada
CoalEvol. Simulation of alignments of nucleotide, codon and amino acid sequences, contemporaneous or not, from populations evolved under a neutral coalescent model with a variety of evolutionary scenarios such as recombination (including recombination hotspots and intracodon recombination), migration, demographics and species/population trees. User specified trees can also be applied. Overall, this simulator implements all features of Recodon and NetRecodon plus many new scenarios.
Current version is 7.3.5
© 2009-2014 Miguel Arenas & David Posada
ProteinEvolver. Simulation of protein evolution along phylogenies under structure-based substitution models
Current version is 1.2.0
© 2013 Miguel Arenas, Helena G. Dos Santos, David Posada & Ugo Bastolla
NetRecodon. Simulation of DNA (coding and non coding) sequences with (inter and intracodon) recombination, migration and demographics
Current version is 6.0.0
© 2009-2011 Miguel Arenas and David Posada
Recodon. Simulation of DNA (coding and non coding) sequences with (intercodon) recombination, migration and demographics
Current version is 1.6.0
© 2007-2011 Miguel Arenas and David Posada
Splatche. Simulation of genetic data (DNA, SNP, STR) under spatially-explicit evolutionary scenarios. In collaboration with Mathias Currat, Claudio Quilodran, Laurent Excoffier and Nicolas Ray (main developers)
Current version is 3.0
ANALYSIS OF GENETIC DATA
Current version is 2.1
© 2013-2020 Miguel Arenas & Ugo Bastolla
CodABC. Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation
Current version is 2.0.0
© 2009-2015 Miguel Arenas, Joao S Lopes, Mark A Beaumont & and David Posada
Current version is 1.0.0
© 2010 Miguel Arenas, Mateus Patricio, David Posada & Gabriel Valiente
