Kew Tree of Life Explorer - Release notes
=========================================

The Kew Tree of Life Explorer allows users to explore evolutionary trees of life and to 
access the genomic data that underpin them. It is an output of the Plant and Fungal Trees 
of Life Project (PAFTOL) at the Royal Botanic Gardens, Kew 
(https://www.kew.org/science/our-science/projects/plant-and-fungal-trees-of-life), which 
aims to discover and disseminate the evolutionary history of all plant and fungal genera 
through phylogenetic approaches.  Tree of Life data are periodically released via the Kew 
secure file transfer protocol (SFTP) site (sftp.kew.org/pub/treeoflife) and are 
additionally made available for interactive web-based exploration at 
http://treeoflife.kew.org.

Data releases are identified with a major and a minor version number, separated by a ".". 
This document describes the contents of Kew Tree of Life Explorer Release 1.0.

Scope and methodology
=====================

This version of the Kew Tree of Life data set comprises data from 64 orders, 404 families, 
2,333 genera and 2,956 species of angiosperms, based on the Angiosperms353 gene set. As a 
result of filtering and trimming steps during alignment, six genes in Data Release 1.0 
were excluded from downstream phylogenetic analysis due to insufficient overlap between 
sequences.  The final tree was produced from the remaining 347 genes.

The phylogenetic approach used in the Tree of Life Explorer has been described here:
https://doi.org/10.1101/2021.02.22.431589.

This release was produced with the software listed below:

Trimmomatic v.0.390 Bolger et al (2014) https://doi.org/10.1093/bioinformatics/btu170
http://www.usadellab.org/cms/?page=trimmomatic

Paftools https://github.com/RBGKew/KewTreeOfLife

UPP Nguyen et al (2015) https://doi.org/10.1186/s13059-015-0688-z 
https://github.com/smirarab/sepp

ASTRAL III Zhang et al Mirarab (2018) https://doi.org/10.1186/s12859-018-2129-y
https://github.com/smirarab/ASTRAL

AMAS Borowiec (2016) https://doi.org/10.7717/peerj.1660 
https://github.com/marekborowiec/AMAS

TreeShrink 1.3.4 Mai and Mirarab (2018) https://doi.org/10.1186/s12864-018-4620-2
https://github.com/uym2/TreeShrink

IQ-TREE 2.0.5 Minh et al (2020) https://doi.org/10.1093/molbev/msaa015 
http://www.iqtree.org/

Newick Utilities 1.6.0 Newick Utilities 1.6.0 Junier and Zdobnov (2010) 
https://dx.doi.org/10.1093%2Fbioinformatics%2Fbtq243  http://cegg.unige.ch/newick_utils

Source nucleotide (DNA or RNA) data, either in the form of raw sequence reads, or 
assembled transcripts or genomes, have either been downloaded from the European Nucleotide 
Archive (ENA), or have been generated by PAFTOL and submitted to the ENA.  A list of ENA 
accession numbers used is included with every release 
(see sftp.kew.org/pub/patfol/README.txt for a description of the contents of each 
release).

Licensing
=========

Kew Tree of Life data (hereafter "the data") are released under the Creative Commons 
Attribution 4.0 International (CC BY 4.0) license 
(https://creativecommons.org/licenses/by/4.0). To attribute the data, please follow our 
citation guidelines (below) and reference the appropriate data release number.

In many cases, the data have been released prior to publication in the academic 
literature, in accordance with the Toronto guidelines on pre-publication data sharing 
(https://www.nature.com/articles/461168a). Users may freely analyse released 
prepublication data, but should act responsibly by 1) respecting the scientific etiquette 
that allows data producers to publish the first global analyses of their data set, 2) 
accurately and completely citing the source of prepublication data, and 3) contacting the 
data producers to discuss publication plans in the case of overlap between planned 
analyses. Please contact us (at the email address below) if you have any questions about 
what you may do with the data.
 
Citing us
=========

When using the Kew Tree of Life Explorer, please cite the following publication:

Baker et al., A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of 
Life. https://doi.org/10.1101/2021.02.22.431589.

Contact us
==========

Please contact treeoflife AT kew DOT org for support or advice.