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Citations per year

Number of citations per year for the bioinformatics software tool Recodon

Tool usage distribution map

This map represents all the scientific publications referring to Recodon per scientific context
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Recodon specifications


Unique identifier OMICS_06853
Name Recodon
Alternative name NetRecodon
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Parallelization MPI
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Miguel Arenas
  • person_outline David Posada

Additional information

Publications for Recodon

Recodon citations


Tracing the origin and evolution of supergene mimicry in butterflies

Nat Commun
PMCID: 5677128
PMID: 29116078
DOI: 10.1038/s41467-017-01370-1

[…] We simulated the evolution of P. polytes dsx nucleotide sequences using NetRecodon. The non-mimetic dsx coding sequence from Papilio polytes v1.0 was used as the grand most recent common ancestor (GMRCA) sequence. A discrete gamma distribution model with three categories […]


A Visualization Tool for Calculating the Genetic Substitution Patterns Between Two Different Groups

Evol Bioinform Online
PMCID: 4517834
PMID: 26279617
DOI: 10.4137/EBO.S28844

[…] protein-coding DNA sequences, which could be implemented for phylogenetic estimation. They used the Markov process to describe substitution between codons. Arenas and Posada developed a program named Recodon that could simulate possible coding DNA sequences under complex scenarios in which several evolutionary forces could be interacting simultaneously. Subsequently, they developed an algorithm th […]


Identification of broadly neutralizing antibody epitopes in the HIV 1 envelope glycoprotein using evolutionary models

Virol J
PMCID: 4220805
PMID: 24295501
DOI: 10.1186/1743-422X-10-347

[…] a simulation study to assess whether a single recombination breakpoint was likely to substantively affect our results. Briefly, we simulated 10 alignments with a single recombination breakpoint using NetRecodon [] and evolved log titers along the phylogeny corresponding to the largest non-recombinant partition of each alignment according to Brownian motion. We applied our method to each of the 10 […]


How Good Are Indirect Tests at Detecting Recombination in Human mtDNA?

PMCID: 3704238
PMID: 23665874
DOI: 10.1534/g3.113.006510
call_split See protocol

[…] a mutation at that site. For our sequences, and assuming μ to be 5 × 10−7, R was estimated at 1.170 giving an r value of 5.8485 × 10−7 (see for more details).These parameters were incorporated into RECODON v1.5.0, which generates sequence under a coalescent model (). Population parameters per locus were estimated from a product of twice the number of inheritable copies, the per-site factor and t […]


Computer Programs and Methodologies for the Simulation of DNA Sequence Data with Recombination

Front Genet
PMCID: 3561691
PMID: 23378848
DOI: 10.3389/fgene.2013.00009

[…] Direct simulation of coding DNA sequences with recombination can be only performed with a few programs. Using the coalescent approach, the programs Recodon (Arenas and Posada, ), CodonRecSim (Anisimova et al., ), and NetRecodon (Arenas and Posada, ) allow such simulation, but only the latter program does not force recombination breakpoints to occ […]


Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets

BMC Evol Biol
PMCID: 2925852
PMID: 20696057
DOI: 10.1186/1471-2148-10-242
call_split See protocol

[…] To evaluate the performance of the four criteria when the generating model is more complex than any of the 56 candidate models, we conducted another simulation (VI) as a special case using Recodon v.1.6.0 []. With the GY94 codon model [] crossed with the settings in parameter set-A for the 24 fundamental models of GTR family respectively, and with the same base frequencies for all codon […]

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Recodon institution(s)
Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain
Recodon funding source(s)
Partially supported by grant BFU2004-02700 (MCyT) and by the FPI fellowship BES-2005-9151 (MEC) from the Spanish government.

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