r8s pipeline

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 Stable
Maintained No

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Publication for r8s

r8s IN pipelines

 (9)
2018
PMCID: 5809883
PMID: 29433445
DOI: 10.1186/s12864-018-4531-2

[…] 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 [39], implemented in r8s v1.81 [40]. the estimated origin time of cyanobacteria (2700~ 3500 million years ago, mya) [41] and the divergence time between escherichia coli and salmonella enterica (140 mya) [42] 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 (sanderson 2003) 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 […]

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, 2003) 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: 5013490
PMID: 27599883
DOI: 10.1038/srep32596

[…] analysis with 1000 replicates was conducted to assess the percentage support for each node. finally, an ultrametric tree was obtained using the non-parametric rate smoothing approach in the r8s software package48., we measured a total of six traits to quantitatively represent several important axes of plant functional strategy. specific leaf area (sla), leaf phosphorus content (lpc) […]

2016
PMCID: 5029880
PMID: 27649395
DOI: 10.1371/journal.pone.0162539

[…] and maximum age constraints, trees (with branch lengths calculated by mrbayes) in the 9 tree files were converted to time trees (with branch lengths scaled to time) using penalized likelihood in r8s version 1.7 [47, 48]. for each tree, the smoothing parameter was optimized using cross-validation and a logarithmic penalty function implemented. trees where the branch lengths had been converted […]

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

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