Recodon statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Recodon
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Tool usage distribution map

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

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Popular tool citations

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Protocols

Recodon specifications

Information


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

Versioning


No version available

Maintainers


  • person_outline Miguel Arenas
  • person_outline David Posada

Additional information


https://github.com/MiguelArenas/netrecodon

Publications for Recodon

Recodon citations

 (9)
library_books

Tracing the origin and evolution of supergene mimicry in butterflies

2017
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 […]

library_books

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

2015
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 […]

library_books

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

2013
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 […]

call_split

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

2013
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 […]

library_books

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

2013
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 […]

call_split

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

2010
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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