The Supertree Toolkit 2
Contents
1. IP rights notes GNU GPL v3 Additional information The STK is available from Launchpad http launchpad net supertree toolkit There are two main bzr branches a stable release version and the development version trunk Contributors are expected to branch trunk develop their new feature and request a merge back into trunk We encourage all such contributions STK is released in GPLv3 and is 10 Hill J Davis K available as source code via Launchpad s PPA system as a Windows and MacOS X binary A full user manual including a tutorial and data for the tutorial are available from the Launchpad website In future we aim to integrate web based taxonomy databases to aid taxonomy and nomenclature standardisation We are also developing a website to release all data that have been collected thus far The STK will be integrated into that online resource Finally we intend to develop a simple tree editing and visualisation GUI such that no external software is required for the whole processing pipeline Acknowledgements The authors wish to thank Steve Mitchell Cyrille Delmer and Matthew Wills all at the University of Bath for help with testing and bug reporting We would also like to thank Carl Boettiger Karen Cranston Graeme Lloyd and Matthew Yoder for comments that helped improve the manuscript Author contributions JH wrote the Supertree Toolkit software and drafted the manuscript KED drafted the manuscript and designed2. ID Tree s 0 tsang_etal_2008_1 Ahyong_etal_2009_1 Ahyong_etal_2009_2 porter_etal_2005_1 cunningham_etal_1992_1 1 2 3 4 5 boyko_harvey_2009_1 6 hall_thatje_2009_1 7 mantelatto_etal_2006_1 8 hiller_werding_2007_1 e 9 mclaughlin_etal_2007_1 10 tirelli_etal_2010_1 11 werding_etal_2001_1 12 cabezas_etal_2009_1 13 cabezas_etal_2009_2 14 cabezas_etal_2009 3 0 2 4 6 8 15 tsang_etal_2011_1 No of connected trees 16 morrison_etal_2002_1 Figure 4 Result of the taxonomic overlap check which highlights which source trees are not sufficiently well connected to the rest of the dataset Data summary This function creates a text summary of the data The summary includes a taxa list years of publication characters used and analyses used Clean data Before and during processing trees may become uninformative i e contain no clades for example after substitution of taxa or when dealing with polyphyletic taxa This function checks that the data are suitable for processing and removes uninformative trees and sources if they contain no trees and should be run regularly on data between processing steps Permute trees When creating supertrees at species level digitised trees need to account for the fact that some species may be polyphyletic There are no formal mechanisms for dealing with this so taxa can be encoded with a d sign to designate them as polyphyletic where d is a consecutive integer for each taxon
3. The permute trees function generates all possible permutations of these trees to enable a consensus tree of some kind to be created Substitute taxa One of the most onerous tasks of supertree creation is ensuring a consistent taxonomy is used throughout This requires the removal of synonyms mis spellings and other naming errors The sub taxa function allows substitution and deletion of taxa whilst maintaining the tree structure Substitutions are aware of polyphyletic taxa and will collapse superfluous nodes when deleting taxa This function is used throughout the processing 8 Hill J Davis K Data independence It has previously been noted that all data included in supertree analyses should be independent of each other Here we defined non independent data as being datasets that contain a subset of the same taxa and use identical characters This function flags source trees that are subsets of others and can automatically remove them if required and flags those that are identical i e same taxa and characters Replace genera This is one of the final steps of the pipeline After all processing some taxa at genus level may be left in the source trees This function replaces those genera with a polytomy of species already in the dataset Note that this assumes a species level tree is to be created and this step can be omitted if this is not the case Data overlap In order to create a supertree all source trees should exhibit
4. The Supertree Toolkit 2 a new and improved software package with a Graphical User Interface for supertree construction Biodiversity Data Journal 2 e1053 doi 10 3897 BDJ 2 e1053 Abstract Building large supertrees involves the collection storage and processing of thousands of individual phylogenies to create large phylogenies with thousands to tens of thousands of taxa Such large phylogenies are useful for macroevolutionary studies comparative biology and in conservation and biodiversity No easy to use and fully integrated software package currently exists to carry out this task Here we present a new Python based software package that uses well defined XML schema to manage both data and metadata It builds on previous versions by 1 including new processing steps such as Safe Taxonomic Reduction 2 using a user friendly GUI that guides the user to complete at least the minimum information required and includes context sensitive documentation and 3 a revised storage format that integrates both tree and meta data into a single file These data can then be manipulated according to a well defined but flexible processing pipeline using either the GUI or a command line based tool Processing steps include standardising names deleting or replacing taxa ensuring adequate taxonomic overlap ensuring data independence and safe taxonomic reduction This software has been successfully used to store and process data consisting of over 1000 trees
5. KE Hill J 2010 The Supertree Tool Kit BMC Research Notes 3 1 95 DOI 10 1186 1756 0500 3 95 Edwards E Still C Donoghue M 2007 The relevance of phylogeny to studies of global change Trends in Ecology amp Evolution 22 5 243 249 DOI 10 1016 j tree 2007 02 002 Gatesy J 2004 A Critique of Matrix Representation with Parsimony Supertrees In Bininda Emonds OP Ed Phylogenetic Supertrees Spinger ISBN 978 1 4020 2329 3 DOI 10 1007 978 1 4020 2330 9 18 Goloboff P Farris J Nixon K 2008 TNT a free program for phylogenetic analysis Cladistics 24 5 774 786 DOI 10 1111 j 1096 0031 2008 00217 x Ham DA Farrell PE Gorman GJ Maddison JR Wilson CR Kramer SC Shipton J Collins GS Cotter CJ Piggott MD 2009 Spud 1 0 generalising and automating the user interfaces of scientific computer models Geoscientific Model Development 2 1 33 42 DOI 10 5194 gmd 2 33 2009 Han MV Zmasek CM 2009 phyloXML XML for evolutionary biology and comparative genomics BMC Bioinformatics 10 1 356 DOI 10 1186 1471 2105 10 356 Helmus M Bland T Williams C Ives A 2007 Phylogenetic Measures of Biodiversity The American Naturalist 169 3 E68 E83 DOI 10 1086 511334 Isaac NB Turvey S Collen B Waterman C Baillie JM 2007 Mammals on the EDGE Conservation Priorities Based on Threat and Phylogeny PLoS ONE 2 3 e296 DOI 10 1371 journal pone 0000296 Jeffery J Wilkinson M 2004 PerlEQ Lloyd GT Davis KE Pisani D Tar
6. UNIVERSITY OF BATH Davis K and Hill J 2014 The Supertree Toolkit 2 A new and improved software package with a Graphical User Interface for supertree construction Biodiversity Data Journal ISSN 1314 2836 Link to official URL if available http dx doi org 10 3897 BDJ 2 e1053 This is the published version of an article published by Pensoft Publishers in Davis K amp Hill J 2014 The Supertree Toolkit 2 A new and improved software package with a Graphical User Interface for supertree construction Biodiversity Data Journal and available via http dx doi org 10 3897 BDJ 2 e1053 Opus University of Bath Online Publication Store http opus bath ac uk This version is made available in accordance with publisher policies Please cite only the published version using the reference above See http opus bath ac uk for usage policies Please scroll down to view the document Biodiversity Data Journal 2 e1053 CO doi 10 3897 BDJ 2 e1053 open access Software description The Supertree Toolkit 2 a new and improved software package with a Graphical User Interface for supertree construction Jon Hillt Katie E Davist t Imperial College London London United Kingdom University of Bath Bath United Kingdom Corresponding author Jon Hill jon hill imperial ac uk Academic editor Matthew Yoder Received 10 Jan 2014 Accepted 25 Mar 2014 Published 26 Mar 2014 Citation Hill J Davis K 2014
7. al and tutorial dataset Filename Tutorial_and_Manual zip Download file 1 32 MB
8. eX format for importing and exporting bibliographic information which is widely supported by references managers We have also added tools to carry out data processing based on those in the original STK Davis and Hill 2010 and extending them to include safe taxonomic reduction Wilkinson 1995 The GUI is split into two vertical panes the left contains a hierarchical view of the data Each row in this hierarchy is an element which can contain a number of nested elements Elements at the same level in the hierarchy can be copy and pasted to aid data entry The right hand side is split into three horizontal panes Fig 1 The uppermost pane displays context sensitive help the middle pane allows for data entry and the lower most pane contains user comments where available All processing functions are 4 Hill J Davis K available in the GUI and use specifically designed interfaces to allow the user to choose options and output processing steps to the file The command line interface contains the processing steps as sub commands Each processing step then contains the options specific to this function As with the GUI documentation is available using standard flags and options Supertree Toolkit Unsaved File Edt View STK Functions Validate Tools Help Node Option Properties poy Project Name v Sources Source Bibliographic Information gt Article Data t Source Tree Tree Taxa Data Character Data Comment His
9. ees which are the input to any supertree algorithm is non trivial as a number of important considerations must be made concerning data quality These issues with supertree analysis including data independence taxonomic overlap and consistent taxonomy have been discussed elsewhere at length Bininda Emonds et al 2004 Bininda Emonds et al 2005 Gatesy 2004 Given the potential large size of datasets and the amount of processing that must be done prior to the supertree analysis being carried out this is not an easy task There is therefore a need for a comprehensive software package that can carry out this prior processing and can preferably store data in a well defined manner Some workers have written and made available scripts that carry out one or more of the required processing steps e g Bininda Emonds et al 2004 Bininda Emonds et al 2005 Davis and Hill 2010 These scripts have a number of drawbacks such as the lack of a user friendly interface and lack of optimisation resulting in slow computationally intensive analyses that take many days or even weeks to run for large datasets Other issues include data format conversion between processing steps for example converting from Newick based tree strings to NEXUS format In addition none of these software scripts include methodologies for collecting metadata a key part of a robust and rigorous processing pipeline An attempt to mitigate these issues led to the creation of the Supertree T
10. irst detail the storage mechanism based on RelaxNG XML and the user interface features We then cover the available processing pipeline steps and show some examples of their use Project description Title Supertree Toolkit STK Design description The STK consists of three components a Python module a Graphical User Interface GUI and a Command Line Interface CLI The python module contains all processing importing and exporting functions These functions deal with the Phyml format see below and are available in any Python environment by importing the supertree_toolkit module The GUI and CLI then import this Python module and hook it to the interface by processing user options In this way the core functionality can be tested by using standard unit test infrastructure and the interfaces are cleanly separated A test suite of over 375tests is included in the source code which benchmark the expected performance of the software User interface There are two user interfaces a GUI for data entry and processing and a CLI for data processing The latter is useful for dealing with large datasets The GUI is based on Diamond Ham et al 2009 which was originally designed for entering user options for numerical modelling software We have extended the capabilities of Diamond to be suitable for entering phylogenetic data A number of specific plugins have been created to import source trees and manage bibliographic sources We use the BibT
11. nd etc Optional information includes conservation status stratigraphic information synonyms and database accession numbers This approach allows copy and pasting of Sources between dataset via the GUI easy navigation of the whole data structure as well as the meta and source tree data being displayed alongside each other This is in contrast to the previous version where files were distributed within sub folders on disk and the tree and meta data were contained in separate files Davis and Hill 2010 BE he Optimality Criterion 4 Outgroup information Bibliographic info Tree string Figure 2 Data structure of the STK metadata Each project consists of several sources which in turn contain bibliographic information and one or more source trees The blue boxes show the hierarchy for a single source tree The data structure has been simplified here and more meta data can be stored for each source tree The result of this schema is a single XML datafile that contains all metadata and source data required This file is termed a Phylml Phylogenetic Meta Language which can be parsed by any standard XML parser 6 Hill J Davis K Processing functions There are a number of processing functions included in the STK These can be chained together to construct a processing pipeline to collect curate and process data Fig 3 The processing functions are Remove higher level taxa Remove non independent data Supert
12. oolkit STK Davis and Hill 2010 a collection of Perl scripts designed to carry out the prior processing required for supertree construction This package was the first to use both source trees alongside their metadata to perform the processing This software however was difficult to use command line only and had only a rudimentary GUI for creating metadata The storage mechanisms chosen required strict naming conventions and therefore was somewhat fragile Moreover the metadata was optional for most of the processing pipeline thereby negating its full value The original STK Davis and Hill 2010 The Supertree Toolkit 2 a new and improved software package with a Graphical 3 whilst a step in the right direction did not therefore meet the requirements for an easy to use rigorous method to collect both metadata and data Here we present the next version of the Supertree Toolkit that builds on the experience of the first version We have rewritten all code and designed the software around a user interface that can carry out both data collection and processing It contains a number of additional features over the original software which are 1 new processing steps such as Safe Taxonomic Reduction 2 user friendly GUI that guides the user to complete at least the minimum information required and includes context sensitive documentation and 3 a revised storage format that integrates both tree and meta data into a single file We will f
13. ready for analyses using standard supertree methods This software makes large supertree creation a much easier task and provides far greater flexibility for further work Hill J Davis K This is an open access article distributed under the terms of the Creative Commons Attribution License CC BY 4 0 which permits unrestricted use distribution and reproduction in any medium provided the original author and source are credited 2 Hill J Davis K Keywords Supertree phylogeny data curation meta data Introduction Supertrees are large phylogenies created by amalgamating anywhere from tens to thousands of smaller source phylogenies A number of algorithms exist for this the most widely used being Matrix Representation with Parsimony Ragan 1992 These algorithms have varying extents of software implementation again with MRP being the most commonly implemented Supertrees have been created for a wide variety of taxonomic groups including birds Cornwallis et al 2010 Davis 2008 dinosaurs Lloyd et al 2008 angiosperms Davies et al 2004 and marsupials Cardillo et al 2004 Large phylogenies are useful for answering questions in macroevolution e g Lloyd et al 2008 comparative biology e g Edwards et al 2007 biodiversity Crozier et al 2005 Helmus et al 2007 and conservation e g Isaac et al 2007 However large scale supertrees are not straightforward to construct Collecting storing and processing the source tr
14. ree analysis vep veao Figure 3 Example of a processing pipeline that can be created with the STK Data are collected and then are put through the processing pipeline in order to create a matrix The resulting matrix in either Nexus format nex or Hennig format tnt can then be analysed in any suitable software such as PAUP Swofford 2003 or TNT Goloboff et al 2008 i Data summary produce text summary of data such as number of taxa trees and characters Clean data check data and remove redundant data such as non informative trees Permute all trees remove non monophyly from trees Substitute taxa perform substitutions or deletions of taxa Data independence check check that all source trees are independent of each other Data overlap check the taxonomic overlap Fig 4 j Replace genera replace generic level taxa with polytomies of all species in that genus that are in the dataset Create matrix create a MRP matrix Baum and Ragan coding of the dataset s Create subset create a subset of this dataset e g only certain years or data types STR perform safe taxonomic reduction on the dataset This is new functionality over the previous version of the STK Davis and Hill 2010 The Supertree Toolkit 2 a new and improved software package with a Graphical 7 Your data are not connected sufficiently at this overlap level Graph Network Tree information
15. sufficient taxonomic overlap Sanderson et al 1998 Data overlap checks this with a user defined overlap minimum is two and can present the results in two graphical formats e g Fig 4 Create subset One of the novelties of the STK is that it can be used to create subsets of the whole dataset based on the metadata For example all trees that used molecular character can be extracted and used to create a new dataset Similarly publication year author or analysis type can all be used to create subsets These can be used to create independent supertrees and the effect of including say only molecular data can be compared to the supertree generated from the whole dataset Create matrix One of the key functions of the STK is to create a matrix for supertree analysis from the input source trees This function can generate a matrix in a number of formats and also output a single treefile containing all trees in the dataset Safe Taxonomic Reduction STR A new function for this version is Safe Taxonomic Reduction STR This is the only new functionality in this version over the previous version Davis and Hill 2010 STR is as detailed by Jeffery and Wilkinson 2004 but has been optimised for use on MRP matrices as an assumption is made that the data only contain 0 1 or as characters This substantially speeds up computation and can process very large datasets consisting of several thousand taxa although run times are still days ra
16. the software References Bininda Emonds O Beck R Purvis A 2005 Getting to the Roots of Matrix Representation Systematic Biology 54 4 668 672 DOI 10 1080 10635150590947113 e Bininda Emonds O Jones KE Price S Cardillo M Grenyer R Purvis A 2004 Garbage in garbage out data issues in supertree construction In Bininda Emonds OP Ed Phylogenetic supertrees combining information to reveal the Tree of Life Kluwer Academic Publishers ISBN 978 1 4020 2329 3 Cardillo M Bininda Emonds OP Boakes E Purvis A 2004 A species level phylogenetic supertree of marsupials Journal of Zoology 264 1 11 31 DOI 10 1017 S0952836904005539 j Cornwallis C West S Davis K Griffin A 2010 Promiscuity and the evolutionary transition to complex societies Nature 466 7309 969 972 DOI 10 1038 nature09335 s Crozier RH Dunnett LJ Agapow P 2005 Phylogenetic biodiversity assessment based on systematic nomenclature Evolutionary bioinformatics online 1 11 36 The Supertree Toolkit 2 a new and improved software package with a Graphical 11 Davies TJ Barraclough TG Chase MW Soltis PS Soltis DE Savolainen V 2004 Darwin s abominable mystery Insights from a supertree of the angiosperms Proceedings of the National Academy of Sciences 101 7 1904 1909 DOI 10 1073 pnas 0308127100 Davis K 2008 Reweaving the Tapestry A supertree of birds University of Glasgow 269 pp URL http theses gla ac uk 178 Davis
17. ther than minutes STR identifies those taxa that give no extra phylogenetic information and recommends their removal from the matrix Wilkinson 2001 describes several categories of taxa that the STR algorithm identifies Of concern are the category C taxa where their removal from the matrix is safe as they do not provide any additional information but can be placed The Supertree Toolkit 2 a new and improved software package with a Graphical 9 back into the supertree post analysis The STK generates a new matrix as well as a text file detailing the categories of all taxa as well as identifying those that can be safely removed In addition a substitution file can also be generated to put category C back into the final supertree once generated Funding KED was funded by BBSRC grant BB K006754 1 and a Systematics Association SynTax grant Building the arthropod supertree interactively Malacostracan crustaceans as a test case 2010 11 funding round awarded to Matthew Wills and Mark Wilkinson Web location URIs Homepage hittp supertreetoolkit org Download page https launchpad net supertree toolkit download Bug database https bugs launchpad net supertree toolkit bugs Technical specification Platform Linux Windows MacOS X Programming language Python Repository Type bzr Browse URI https code launchpad net supertree toolkit Location Ip supertree toolkit Usage rights Use license Other
18. tory Figure 1 The STK GUI based on Diamond Ham et al 2009 The GUI is split into two main panes with the left being used to store data and the right showing the context based help top data entry middle and comments bottom We have maintained all the previous functionality of the previous version of the STK which are detailed in Davis and Hill 2010 We therefore restrict ourselves to a brief description of the functionality and describe new functionality in detail Safe Taxonomic Reduction Metadata and file format XML is an ideal way to store structured metadata We build on the methods used by Spud Ham et al 2009 using the RelaxNG method to create a data schema This schema dictates what information the user interface shows the options in the left hand side of the GUI Fig 1 are generated on the fly from this schema and aids the user in two ways First data can be defined as required or optional within the schema and the interface highlights required data accordingly Second context sensitive documentation is embedded in the schema and is shown in the user interface The user does not interact directly with the schema but the schema dictates which data can be stored and what is shown in the user interface The base schema is a human readable file in compact RelaxNG format It is this file where required and optional GUI elements can be added as well as context senstivie documentation Software spud preprocess dis
19. tributed as part of Spud Ham et al 2009 then transforms this into a full XML file The two files one a rnc the other a rng are distributed along with the GUI to generate the user interface The GUI then reads this XML files the rng file otherwise known as the schema to display options The Supertree Toolkit 2 a new and improved software package with a Graphical 5 to the user The file the user saves is therefore linked to this schema as the schema dictates the data that can be displayed and entered via the GUI and hence saved in a file There are a number of other file formats that allow the user to store both trees and their metadata such as NexML Vos et al 2012 and PhyloXML Han and Zmasek 2009 We have written the code so that the GUI can be automatically generated from our XML schema but not NeXML or PhyloXML however parsers to import from and export to these file formats will be added in future versions The schema used here is easily extensible and was designed with initiatives such as MIAPA in mind which was used to define the terms used though not in a formal manner Each dataset has a name and contains a number of Sources Fig 2 Each source is a publication and includes the bibliographic information followed by one or more Source Trees Each Source Tree then contains the tree string the characters and methods used to create the tree along with information on fossil taxa and other metadata figure number lege
20. ver JE Ruta M Sakamoto M Hone DW Jennings R Benton MJ 2008 Dinosaurs and the Cretaceous Terrestrial Revolution Proceedings of the Royal Society B Biological Sciences 275 1650 2483 2490 DOI 10 1098 rspb 2008 0715 Ragan M 1992 Phylogenetic inference based on matrix representation of trees Molecular Phylogenetics and Evolution 1 1 53 58 DOI 10 1016 1055 7903 92 90035 F Sanderson M Purvis A Henze C 1998 Phylogenetic supertrees Assembling the trees of life Trends in Ecology amp Evolution 13 3 105 109 DOI 10 1016 0169 5347 97 01242 1 Swofford DL 2003 PAUP Phylogenetic Analysis Using Parsimony and Other Methods 4 Sinauer Associates Sunderland Massachusetts Vos RA Balhoff JP Caravas JA Holder MT Lapp H Maddison WP Midford PE Priyam A Sukumaran J Xia X Stoltzfus A 2012 NeXML rich extensible and verifiable representation of comparative data and metadata Systematic Biology 61 4 675 689 DOI 10 1093 sysbio sys025 12 Hill J Davis K Wilkinson M 1995 Coping with Abundant Missing Entries in Phylogenetic Inference Using Parsimony Systematic Biology 44 4 501 514 DOI 10 1093 sysbio 44 4 501 Wilkinson M 2001 TAXEQ3 Software and documentation Natural History Museum London Supplementary material Suppl material 1 Manual and tutorial data Authors Jon Hill and Katie Davis Data type Mix PDF nex and phyml Brief description The STK User manu
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