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ERaBLE specifications

Information


Unique identifier OMICS_10977
Name ERaBLE
Alternative name Evolutionary Rates and Branch Length Estimation
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data ERaBLE requires at least two input files: one matrices file and one tree topology file.
Output data ERaBLE outputs two outfiles: (i) the topology in NEWICK format with the branch lengths computed by ERaBLE with the suffix ".lengths.nwk", (ii) the gene rates with the suffix ".rates.txt".
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Fabio Pardi <>

Publication for Evolutionary Rates and Branch Length Estimation

ERaBLE in publications

 (8)
PMCID: 5751766
PMID: 29297348
DOI: 10.1186/s12870-017-1195-z

[…] interchange was used. distance matrices were calculated using baseml/codeml trees in the ape package []. then relative evolution rate for each region (coding and non-coding) was calculated using erable []. sliding window analysis (window = 200 b.p.) of p-distances, i.e. the proportion of nucleotide differences per site between sequences was calculated by perl script made by masafumi nozawa […]

PMCID: 5743822
PMID: 28925584
DOI: 10.1111/1751-7915.12797

[…] such as acidithiobacillus ferrooxidans can oxidize iron under strict aerobic conditions. moreover, as electrocatalytic reduction in o2 to h2o is kinetically limited by the availability of protons (erable et al., ), a. ferrooxidans offers a great prospect for air biocathode design (ter heijne et al., ; carbajosa et al., ; rodrigues and rosenbaum, ; ishii et al., )., acidithiobacillus […]

PMCID: 4768163
PMID: 26917470
DOI: 10.1038/srep22194

[…] fund for scientific research (f.r.s. - fnrs, belgium). a.v., j.f.g. and s.m. are grateful to the walloon region for financial support in the frame of the batwal “programme d’excellence” and “erable” programme. this research connects to the arc project entitled “tintin” (no. 09/14-023) sponsored by the communauté francaise de belgique and to the f.r.s.- fnrs project entitled […]

PMCID: 4767289
PMID: 26863985
DOI: 10.1111/1751-7915.12340

[…] as novel biocatalysts. microbial electron uptake from solid materials is being pursued as biocatalysts for cathode reactions in diverse microbial electrochemical systems (rabaey and rozendal, ; erable et al., ; kim et al., ). based on this idea, cathodic methane production by a corrosive methanogen has already been examined (beese‐vasbender et al., ). close relatives of a corrosive acetogen […]

PMCID: 4802824
PMID: 26474966
DOI: 10.1093/femsre/fuv044

[…] ). an advantage of a low ph mes is that the protons will not cause diffusion limitations in the cathode compartment for reduction of oxygen and therefore, will not limit the current production (erable, etcheverry and bergel ). however, a consequence of growth at low ph is that the cells have to maintain a near neutral cytoplasm (reviewed in slonczewski et al.). this consumes a portion […]


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ERaBLE institution(s)
Laboratoire d’Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), CNRS, Université de Montpellier, Montpellier, France; Institut de Biologie Computationnelle, Montpellier, France; Institut des Sciences de l’Evolution de Montpellier, CNRS, IRD, EPHE, Université de Montpellier, France
ERaBLE funding source(s)
The Labex NUMEV; the EC H2020 project VIROGENESIS (grant number 634650)

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