Recodon protocols

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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


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Maintainers


  • person_outline Miguel Arenas <>
  • person_outline David Posada <>

Additional information


https://github.com/MiguelArenas/netrecodon

Publications for Recodon

Recodon in pipeline

2008
PMCID: 2579306
PMID: 18840286
DOI: 10.1186/1471-2105-9-421

[…] a total of 11 recombination breakpoints, and hence, the strains consist of 12 gene fragments with differing evolutionary histories. the evolutionary trees for the fragments were obtained from recodon output. we used drawgram program included in phylip software package [] to draw the trees. an example of such a tree is shown in figure for the second gene fragment. remaining trees […]


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Recodon in publications

 (10)
PMCID: 5677128
PMID: 29116078
DOI: 10.1038/s41467-017-01370-1

[…] strength of nfds (z = 0.25) because this resulted in a high, but never fixed, mimetic allele frequency in scenario 2., 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 […]

PMCID: 4517834
PMID: 26279617
DOI: 10.4137/EBO.S28844

[…] 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 […]

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

[…] 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 […]

PMCID: 3796270
PMID: 24133504
DOI: 10.3389/fgene.2013.00206

[…] tools exist to simulate and infer args., from the simulation perspective, to my knowledge, only two programs can output a simulated arg, namely, serial netevolve (buendia and narasimhan, ) and netrecodon (arenas and posada, ). most of simulation tools only simulate a tree for each recombinant fragment, but these trees can be then combined to generate the arg by using tools like […]

PMCID: 3704238
PMID: 23665874
DOI: 10.1534/g3.113.006510

[…] 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 […]


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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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