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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

Versioning


No version available

Maintainer


This tool is not available anymore.

Publication for r8s

r8s citations

 (186)
library_books

Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV

2018
Front Microbiol
PMCID: 5938362
PMID: 29765366
DOI: 10.3389/fmicb.2018.00854

[…] as 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 […]

library_books

Pathogenic adaptations of Colletotrichum fungi revealed by genome wide gene family evolutionary analyses

2018
PLoS One
PMCID: 5915685
PMID: 29689067
DOI: 10.1371/journal.pone.0196303

[…] 8.1.1 [] 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 were chos […]

library_books

Comparative Genomics Reveals Thousands of Novel Chemosensory Genes and Massive Changes in Chemoreceptor Repertories across Chelicerates

2018
Genome Biol Evol
PMCID: 5952958
DOI: 10.1093/gbe/evy081

[…] nated 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) […]

library_books

Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios

2018
BMC Genomics
PMCID: 5809883
PMID: 29433445
DOI: 10.1186/s12864-018-4531-2

[…] dy 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 as calib […]

library_books

A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

2018
Sci Rep
PMCID: 5792627
PMID: 29386578
DOI: 10.1038/s41598-018-20154-1

[…] a concatenated alignment of all one-to-one orthologs for branch length estimation. Finally, to generate an ultrametric species tree with branch lengths in millions of years (my) we used the software r8s, with a calibration range based on age estimates of a crown Coleopteran fossil at 208.5–411 my. This calibration point itself was estimated in a similar fashion in a larger phylogenetic analysis o […]

library_books

Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo and autopolyploidization events

2018
BMC Biol
PMCID: 5785856
PMID: 29370802
DOI: 10.1186/s12915-018-0482-y

[…] 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), Sesam […]

Citations

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

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