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CIPRES Science Gateway specifications


Unique identifier OMICS_33418
Name CIPRES Science Gateway
Alternative name Cyberinfrastructure for Phylogenetic Research Science Gateway
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Version 3.3
Stability Stable
Maintained Yes


  • CIPRES Portal
  • CRA

Publication for Cyberinfrastructure for Phylogenetic Research Science Gateway

CIPRES Science Gateway citations


Cryptic diversity: Two morphologically similar species of invasive apple snail in Peninsular Malaysia

PLoS One
PMCID: 5937749
PMID: 29734361
DOI: 10.1371/journal.pone.0196582
call_split See protocol

[…] 2nd codon, and TIM1+G for 3rd codon. These parameters were used to specify the models of sequence evolution, and as priors for Bayesian analysis. Bayesian inference were run in MrBayes v.3.2.1 [] on CIPRES portal [] (Miller et al., 2010) with the following setting: mcmc negen = 10000000; nchains = 4; samplefreq = 100; average deviation of split frequencies < 0.01; and a burn-in value of 25%. The […]


Gymnosperms on the EDGE

Sci Rep
PMCID: 5902588
PMID: 29662101
DOI: 10.1038/s41598-018-24365-4
call_split See protocol

[…] bsequent analyses were performed on the resulting supermatrix. A phylogenetic tree was reconstructed using the maximum likelihood (ML) criterion as implemented in the software RAxML (v. 8.2.8) on the CIPRES portal ( with 1,000 rapid bootstrap replicates followed by the search of the best ML tree. The GTRCAT model was used and all the other parameters were set as default settings. All […]


Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South Western China Reveals Genetic Diversity Loss during the Holocene

PMCID: 5924540
PMID: 29642393
DOI: 10.3390/genes9040198
call_split See protocol

[…] Phylogenetic relationships among the 54 sampled giant panda sequences, as well as their position within the larger Ursid phylogeny, were inferred by maximum likelihood in RAxML-HPC v.8 [] on the CIPRES portal []. Canis lupus familiaris served as an outgroup to root the tree. The D-loop sequences were not used for this analysis due to the possibility of saturation and ambiguous alignment of di […]


Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase

Sci Rep
PMCID: 5869587
PMID: 29588502
DOI: 10.1038/s41598-018-23575-0

[…] rees were inferred using MrBayes v3.2.6 with the WAG + Γ + I substitution model, 1 × 106 generations, sampling frequency of 100, and burn-in fraction of 25%. The phylogenetic analyses were run at the CIPRES Portal (; ref.). The trees were visualized using iTOL (; ref.) and further adjusted with a graphical editor. […]


Molecular and morphological data of the freshwater fish Glandulocauda melanopleura (Characiformes: Characidae) provide evidences of river captures and local differentiation in the Brazilian Atlantic Forest

PLoS One
PMCID: 5868800
PMID: 29579069
DOI: 10.1371/journal.pone.0194247

[…] but lognormally distributed among lineages []. A random tree was used as a starting tree for the MCMC searches and eight chains were run simultaneously. The above analysis was performed twice in the CIPRES portal. The distribution of log-likelihood scores was examined to determine the stationary phase for each search and to decide whether extra runs were required to achieve convergence using Trac […]


Trait and phylogenetic diversity provide insights into community assembly of reef‐associated shrimps (Palaemonidae) at different spatial scales across the Chagos Archipelago

Ecol Evol
PMCID: 5916300
PMID: 29721283
DOI: 10.1002/ece3.3969
call_split See protocol

[…] species in the metacommunity. Phylogenetic trees were constructed under Bayesian Inference (BI) analysis in MrBayes v.3.2 (Ronquist et al., ) (see Table for models of evolution used), on the online CIPRES Science Gateway (Miller & Schwartz, ) for the consensus alignment and for each gene tree separately. A composite metacommunity phylogeny was produced in APE using the phylogeny (Figure ; Paradi […]


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CIPRES Science Gateway institution(s)
San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA; J. Craig Venter Institute, La Jolla, CA, USA; Northrop Grumman Health Solutions, Rockville, MD, USA; Whirl-i-gig, Brooklyn, NY, USA; Department of Anatomical Sciences, Stony Brook University, Stony Brook, NY, USA
CIPRES Science Gateway funding source(s)
Supported by NSF DBI-1262628 and a generous award (TG-DEB090011) of the XSEDE project, NSF DEB−1208270, an NIAID contracts HHSN272200900041C and HHSN272201400028C, and by NIH GM73931-01.

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