ArticleBMC bioinformatics2014
Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- LinguaPhylo: A probabilistic model specification language for reproducible phylogenetic analyses.PLoS computational biology · 2023Article
- The highest-elevation frog provides insights into mechanisms and evolution of defenses against high UV radiation.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Uncoupling transcription and translation through miRNA-dependent poly(A) length control in haploid male germ cells.Development (Cambridge, England) · 2022Article
- Transcriptional identification of genes light-interacting in the extraretinal photoreceptors of the crayfishZooKeys · 2021Article
- NGPhylogeny.fr: new generation phylogenetic services for non-specialists.Nucleic acids research · 2019Article
- Bioinformatic Workflows for Generating Complete Plastid Genome Sequences-An Example fromLife (Basel, Switzerland) · 2018Article
- Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce.Plant physiology · 2018Article
- Colorful seashells: Identification of haem pathway genes associated with the synthesis of porphyrin shell color in marine snails.Ecology and evolution · 2017Article
- A Primer on Infectious Disease Bacterial Genomics.Clinical microbiology reviews · 2016Review
- ReproPhylo: An Environment for Reproducible Phylogenomics.PLoS computational biology · 2015Article
- Opsins in Limulus eyes: characterization of three visible light-sensitive opsins unique to and co-expressed in median eye photoreceptors and a peropsin/RGR that is expressed in all eyes.The Journal of experimental biology · 2015Article
- Evolutionary relatedness does not predict competition and co-occurrence in natural or experimental communities of green algae.Proceedings. Biological sciences · 2015Article
- Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms.BMC bioinformatics · 2014Article
- Ocular and extraocular expression of opsins in the rhopalium of Tripedalia cystophora (Cnidaria: Cubozoa).PloS one · 2014Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPhylogenetic tools and 'tree-thinking' approaches increasingly permeate all biological research. At the same time, phylogenetic data sets are expanding at breakneck pace, facilitated by increasingly economical sequencing technologies. Therefore, there is an urgent need for accessible, modular, and sharable tools for phylogenetic analysis.
resultsWe developed a suite of wrappers for new and existing phylogenetics tools for the Galaxy workflow management system that we call Osiris. Osiris and Galaxy provide a sharable, standardized, modular user interface, and the ability to easily create complex workflows using a graphical interface. Osiris enables all aspects of phylogenetic analysis within Galaxy, including de novo assembly of high throughput sequencing reads, ortholog identification, multiple sequence alignment, concatenation, phylogenetic tree estimation, and post-tree comparative analysis. The open source files are available on in the Bitbucket public repository and many of the tools are demonstrated on a public web server (http://galaxy-dev.cnsi.ucsb.edu/osiris/).
conclusionsOsiris can serve as a foundation for other phylogenomic and phylogenetic tool development within the Galaxy platform.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.