Phylotastic statistics

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Phylotastic specifications

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Information

Unique identifier	OMICS_23509
Name	Phylotastic
Interface	Web user interface
Restrictions to use	None
Input data	An url, a document or a taxon.
Input format	TXT,ZIP,PDF
Output data	A tree.
Programming languages	Java, Javascript, Perl, PHP, Python, R, SPARQL, awk
License	BSD 3-clause “New” or “Revised” License, GNU General Public License version 3.0, MIT License
Computer skills	Basic
Stability	Stable
Maintained	Yes

Documentation

Video: https://youtu.be/S7rGIlFo03o

Maintainers

Van Nguyen <>
Arlin Stoltzfus <>

Additional information

http://phylo.cs.nmsu.edu:3000/static_pages/help

Publications for Phylotastic

Phylotastic: improving access to tree-of-life knowledge with flexible, on-the-fly delivery of trees.

2018 BioRxiv

DOI: 10.1101/419143

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

2013 BMC Bioinformatics

PMCID: 3669619

PMID: 23668630

DOI: 10.1186/1471-2105-14-158

Phylotastic in publications

(3)

Toward a Self Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa

PMCID: 5410925

PMID: 27616324

DOI: 10.1093/sysbio/syw066

[…] units for ancestral range analyses (; töpel et al., this issue); the estimation of rates of migration, speciation, and extinction; extracting subtrees from global species-level chronograms (http://phylotastic.org); among numerous other macroevolutionary and biogeographical analyses, some of which are exemplified here for the palms., our approach for inferring phylogenies first produces […]

The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high throughput sequencing data

PMCID: 3922334

PMID: 24502833

DOI: 10.1186/1471-2105-15-44

[…] in python and uses the biopython[], beautiful-soup[] and requests[] packages to handle fasta sequences and communicate with the various apis and web services used, such as ncbi genbank and the phylotastic tnrs service. the steps of the pipeline are shown in figure and are explained in more detail below., as an offline process, a local database is maintained containing the ncbi taxon ids […]

Advancing data reuse in phyloinformatics using an ontology driven Semantic Web approach

PMCID: 3980757

PMID: 24565381

DOI: 10.1186/1755-8794-6-S3-S5

[…] 2011 [], the w3c workshop on data and services integration [], translational medicine conference at amia 2012 [,] and ieee international conference on bioinformatics and biomedicine []. recent "phylotastic" hackathons [] have also developed resources to promote the reuse of published trees and underlying metadata., other prior art with regard to the semantic web-ready definition […]

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Phylotastic institution(s)

Department of Computer Science, New Mexico State University, Box 30001, MSC CS, Las Cruces, NM, USA; Institute for Bioscience and Biotechnology Research, Rockville, MD, USA; Ft. Lauderdale Research and Education Center, University of Florida/IFAS, Davie, FL, USA; Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA; Illinois Natural History Survey, Species File Group, University of Illinois, Champaign, IL, USA; Office of Data and Informatics, NIST, Gaithersburg, MD, USA

Phylotastic funding source(s)

Supported by funding from the US National Science Foundation (award 1458572).

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