r8s protocols

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r8s specifications

Information


Unique identifier OMICS_15865
Name r8s
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The sequence data.
Output data A simple text plots of trees with or without time calibrations, and Nexus style output of tree descriptions with time-calibrated branch lengths.
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability No
Maintained No

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Publication for r8s

r8s in pipelines

 (15)
2018
PMCID: 5809883
PMID: 29433445
DOI: 10.1186/s12864-018-4531-2

[…] among the noncore region, in order to investigate the unique properties of them., a chronogram for 23 taxa raxml phylogeny was constructed using the method of penalized likelihood [], implemented in r8s v1.81 []. the estimated origin time of cyanobacteria (2700~ 3500 million years ago, mya) [] and the divergence time between escherichia coli and salmonella enterica (140 mya) [] were used […]

2018
PMCID: 5952958
PMID: 29788250
DOI: 10.1093/gbe/evy081

[…] all msa, keeping the individual coordinate information to be used as a partition for the phylogenetic analysis. we used raxml software (option –f e) to obtain ml estimates of branch lengths and r8s software v 1.80 () to linearize the unrooted ml using the penalized likelihood algorithm. for the last step, we constrained the ages of two internal nodes according to the fossil calibrations: 1) […]

2017
PMCID: 5345361
PMID: 28331401
DOI: 10.3897/zookeys.656.11440

[…] were calculated and generated by dnasp (), and an ml tree was constructed by raxml () with haplotype data. due to the ultrametric and bifurcating requirement, the ml tree was constructed with r8s (). the outcome tree modified by r8s was read into the “splits” r package, and the delimiting result was obtained with relevant commands., the poisson tree process (ptp) () model is another […]

2017
PMCID: 5733559
PMID: 29321791
DOI: 10.3389/fpls.2017.02134

[…] supermatrix and the constraint tree. node support was estimated using bootstrap values with 500 replicates. finally, we calibrated the branch lengths of this ml phylogenetic tree using the program r8s v1.70 (sanderson, ) with the nprs method, which was employed in the analysis of the phylogenetic structure of plant communities. we used seven fossil calibration points. minimum ages were set […]

2016
PMCID: 4712825
PMID: 26688468
DOI: 10.1016/j.fgb.2015.12.006

[…] uploaded in ncbi, exonerate () was used to locate the proteins within the genome. identity between proteins of the reference gene cluster and the homologous proteins was calculated using trimal ()., r8s-pl () was used to calculate divergence times among the considered species. the species tree calculated from the phylome was calibrated using the node where sordariomycetes and leotiomycetes […]


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r8s in publications

 (90)
PMCID: 5938362
PMID: 29765366
DOI: 10.3389/fmicb.2018.00854

[…] the general time-reversible substitution model with a four-bin gamma rate distribution (gtr+γ4) (; )., estimate of divergence times was performed by a penalized-likelihood (pl) method implemented in r8s (), using the abs-rel tree as the input tree. in the case of 3 extremely long (i.e., more than 50 substitution/site) terminal branches, most likely resulting from low precision in point estimates […]

PMCID: 5915685
PMID: 29689067
DOI: 10.1371/journal.pone.0196303

[…] [] using the lg+g+i model chosen by prottest version 3.4 [] with the bootstrap value set as 1,000., based on the ml dendrogram generated above, a calibrated species tree was constructed with the r8s software version 1.7 [], analyses were based on penalized likelihood method and the tn algorithm. the colletotrichum crown, sordariomycetes crown, and sordariomycetes-leotiomycetes crown […]

PMCID: 5785856
PMID: 29370802
DOI: 10.1186/s12915-018-0482-y

[…] olive and oleaster. also, we calculated the 4dtv values for each paralogous pair at the branches a, c, and e as marked in additional file : figure s11a., divergence times were calculated using r8s-pl 1.81 []. four nodes were taken as calibration points. the divergence times of these nodes were obtained from the timetree database []: mimulus guttatus and arabidopsis thaliana (117 mya), […]

PMCID: 5798147
PMID: 29360978
DOI: 10.1093/gbe/evy013

[…] across the best ml tree, and estimated the divergence times of the major amniote lineages, including the tmrca of anole lizards, using the semiparametric method based on penalized likelihood (pl) in r8s v1.8 (, ). we used two sets of criteria to constrain minimum, maximum, or fixed node ages. the first set of criteria was based on constraints from the paleontological literature; specifically, […]

PMCID: 5750222
PMID: 29295979
DOI: 10.1038/s41467-017-02441-z

[…] phylogeny in raxml v8.29 (protgammalg; 1000 bootstrap replicates) from 822 concatenated gene models. to estimate time of evolutionary divergence, node calibrations from beimforde et al. were used in r8s v1.80; leotiomycetes–sordariomycetes 267–430 mya, eurotiomycetes 273–537 mya, sordariomycetes 207–339 mya, and pezizomycotina 400–583 mya (supplementary data ). this analysis illustrates […]


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r8s institution(s)
Section of Evolution and Ecology, University of California, Davis, CA, USA

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