A navigation guide to cyberinfrastructure tools for botanical and lichenological systematics research

This website represents a navigation guide to the vast frontier of cyberinfrastructure available for systematics research, specifically for plants and lichens. This guide specifically addresses the interests of new graduate students; however, it should be useful for established researchers as well as interdisciplinary researchers who have an interest in systematics. Included in this guide are 94 websites distributed in 15 categories, each with a brief description. We encourage other disciplines to develop similar navigation guides and suggest that such guides can serve as an important resource for students and early career professionals. If you use this website, please cite our manuscript as follows: Gostel, M. R., M. Dal Forno, and A. Weeks. 2013. A navigation guide to cyberinfrastructure tools for botanical and lichenological systematics research. Plant Science Bulletin. 59(3):111–130. doi: 10.3732/psb.1300001. If you would like to submit a new resource to this page or add a correction, update, or change please contact Morgan Gostel at gostelm [AT] gmail [DOT] com Site updated: 4 November 2016

"What taxa might be present at my study site?"

1 Checklists

These lists describe which species are present in a certain locality, but also what species are not registered for that place yet. They are certainly not static, since new observations can always be added. It provides information to develop hypothesis about how species are related to that habitat they grow and how much biodiversity there is. They also help in establishing species range and distribution around the globe.


Catalogue of Life (CoL): http://www.catalogueoflife.org/
      Catalogue of Life is a partnership linked with several other important projects related to biodiversity (such as GBIF and EOL, described further on) and aims to have an integrated checklist of all living organisms on Earth. There are 1.3 millions species included already, about 70% of the known species. CoL can be used to look up species, to size higher taxa, to check synonyms and related taxa, as well as compile checklists.

Kew World Checklists of Selected Plant Families (WCSP): http://apps.kew.org/wcsp/home.do
      WCSP contains updated checklists of 173 plant families in different stages of completion. Users can also develop their own checklists using a tool on the site by selecting the family and genus in study as well as the continent and region of interest creating a summary or detailed checklist according to one’s settings.

North American Lichen Checklists (Esslinger, 2011): http://www.ndsu.edu/pubweb/~esslinge/chcklst/chcklst7.htm
      A curated checklist for the lichen-forming, lichenicolous and allied fungi of continental United States and Canada with 5246 species currently included. It is a cumulative project since the original version first posted online in 1997 with 3580 species and it has been been yearly updated by Dr. Theodore L. Esslinger at North Dakota State University.

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"Where can I find high quality images of my taxa? Are there interactive learning tools available online to help reinforce difficult concepts and classroom material?"

2 Visual and Other Multimedia

Audio, visual, and multimedia resources are critical to integrating systematics research by providing rich, descriptive information for taxa of interest as well as their habitat. AVM resources include databases and interactive galleries with photos and/or lectures.


Arkive - Images of Life on Earth: http://www.arkive.org/
      Arkive is a project to centralize a digital image library from organisms across different domains of life, but with an emphasis in creating an imagery library of endangered species before they move towards extinction. It has high quality videos and photographs of algae, plants, fungi (including lichens) and animals in nature and/or as voucher specimens.

Inside Wood: http://insidewood.lib.ncsu.edu/welcome
      Inside wood is a project to promote knowledge in wood anatomy. This site is useful for both research and teaching applications, with a search tool and large image database. It can be very useful in systematics since the website provides an interactive key with over 200 features of wood anatomy that can help one to identify the material of study.

Lichens Home Page – Sharnoff Photos: http://www.sharnoffphotos.com/lichens/lichens_home_index.html
      This website offers a reliable photo collection to help the user to identify more than 1,200 lichens of North America. The website is linked to the most up-to-date North American Lichen Checklist and it was developed in combination of two lichen photographers and several lichenologists. The photographs were taken in the development of the book Lichens of North America (Brodo, Sharnoff and Sharnoff 2001).

Morphbank: http://www.morphbank.net/
      Morphbank is a free database containing hundreds of thousands of specimen-based biological images. Morphbank images are maintained for both educational and research purposes.

Pictures of tropical lichens: http://www.tropicallichens.net/
      The largest collection of pictures of tropical lichens online. A searchable list of thousands of species with photo credits, locality data. Photos are organized by genus and species. It is maintained by several lichenologists around the world and it is linked to Index Fungorum and GBIF as well (both databases are listed, below).

Texas A&M University Vascular Plant Image Library: http://botany.csdl.tamu.edu/FLORA/gallery.htm
      An organized list gallery of vascular plant images by taxa. The gallery is organized alphabetically, first by family and then by genus.

Ways of Enlichenment: http://www.waysofenlichenment.net/lichens/gallery.html
      This site provides a regularly updated database of lichen images, which is searchable by several criteria.

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"Where can I find relevant information about the taxa I am working on?"

3 General, Plant and Lichen Biodiversity

In this section, we aim to help people in finding important information about the organisms in study and related taxa. Most of these resources are websites that contain digital books, voucher specimens belonging to important collections, links to other sites, repositories of image and other databases, all working towards distribution of biodiversity knowledge through the web.


3a Biodiversity data – the following resources will help one to find information on the taxa you are working on.

Angiosperm Phylogeny Website: http://www.mobot.org/MOBOT/Research/APweb/welcome.html
      A searchable website and tool for up-to-date information on angiosperm phylogenetics, hosted through the Missouri Botanical Garden. This site is organized according to ordinal-classification and taxa are searchable on a scrolling left-hand panel. Detailed information for an abundance of taxa is available through this Angiosperm Phylogeny website.

Biodiversity Heritage Library: http://www.biodiversitylibrary.org/<
      A consortium of natural history libraries with the goal of providing thousands of historical biological documents online. The digitization of bibliography helps users find old and new literature, which may be otherwise hard to find and encourages the legacy of literature to continue. One can browse by author, year, subject, titles, languages, among other search criteria.

Cyberliber: an Electronic Library for Mycology: http://www.cybertruffle.org.uk/cyberliber/index.htm
      Cyberliber is a digital library dedicated mainly to Fungi. There are several books, journals and catalogues available online as well as a search tool to find literature about the study taxa.

Encyclopedia of Life (EoL): http://eol.org
      The Encyclopedia of Life is a publicly accessible catalog and database of natural history information that was initiated in 2007 with the goal of developing “a webpage for every species”. With several collaborating institutions, EoL actively pursues this goal, but has a stated priority list for taxa of greatest interest. The Encyclopedia of Life continues to be updated and is growing resource for researchers and those with passing interest in biodiversity, alike. The EoL contains nomenclatural, phylogenetic, and visual and multimedia content for taxa. Much of the content is collected from other web-based biodiversity resources, such as GBIF, Tropicos, etc.

Global Biodiversity Information Facility (GBIF): http://www.gbif.org/
      GBIF is a freely accessible resource for biodiversity information, including taxa, distribution, and digistization services. Much of GBIF’s data is shared with and retrieved in other web-based biodiversity resources, such as Discover Life, above.

General MOBOT Resources: http://www.mobot.org/mobot/research/alldb.shtml
      General botanical resources available through the Missouri Botanical Garden’s website. It hosts several links to regional floras (linked to tropicos.org), but additional databases with valuable information about plants.

ITALIC - The Information System on Italian Lichens: http://dbiodbs.univ.trieste.it/
      ITALIC has information on lichens from several regions of Italy but also from other European countries. The highlight of this project are the interactive keys, which can be a useful option for new students from anywhere in the world to learn more about morphology and anatomy of lichens, because they have photographs of different lichen characteristics that are easily observed with the provided images. Users need to register for a free account to access the content.

JSTOR Plant Science: http://about.jstor.org/content-collections/primary-sources/jstor-plant-science
      A digital archive and repository of plant science resources, specializing in historical collections. Contains numerous images and type collections, as well as digitized Floras. Priorities currently include the digitization of type specimens, among which the digitization of 2.2 million specimens is expected by 2013. Other resources, such as regional floras are also available.

Kew Science and Research Resources: http://www.kew.org/science-research-data/index.htm
      The Royal Botanical Gardens, Kew has a website dedicated to promote their global research programs and also distribute general scientific information, such as: photographs, videos, collections data, and more.

Recent Literature on Lichens: http://nhm2.uio.no/botanisk/lav/RLL/RLL.HTM
      This website contains a comprehensive list of published literature about lichens. It is updated often and in September 2016 it contained 47,674 titles; therefore, it is a valuable tool for finding current publications pertaining to lichens.

Tropicos: http://www.tropicos.org/
      Tropicos is a web-based database and information network maintained by the Missouri Botanical Garden. Tropicos contains specimen, nomenclature, distribution, and other reference data for plant specimens from around the world.

3b Biodiversity Tools–

Discover Life: http://www.discoverlife.org
      Discover Life is an initiative for educators and researchers, which provides web-based tools for teaching and learning about biodiversity. Both classroom and more complex research projects can be facilitated with tools available through the site, which includes tools for developing labels, field guides, and maps as well as storage capacity for images of taxa, and locality information. Data for accessions can be uploaded and linked to a particular accession for fast map generation, labeling, etc.

Internet Directory for Botany (IDB): http://www.ou.edu/cas/botany-micro/idb-alpha/botany.html
      The IDB is an extensive catalog of botany-related websites, organized alphabetically. Numerous gardens, guides, checklists, organizations, and other databases and references are included and the list is searchable.

CyVerse: http://www.cyverse.org/
      CyVerse, formerly the iPlant Collaborative, is a cyberinfrastructure development initiative for plant and evolutionary biology. This collaborative facilitates and promotes collaboration, learning, and research in plant science. Educational and research resources developed and hosted by members of the CyVerse team include evolutionary developmental projects, genomics, and phylogenetics. Several tools continue to be developed and updated and researchers can utilize information resources such as cloud computing and storage on the iPlant Atmosphere service. iPlant also offers community networking tools for collaboration across the plant sciences.

Symbiota: http://symbiota.org
      Symbiota provides software tools for biodiversity communication. Symbiota packages facilitate the development of electronic floras and faunas, keys, and other resources for improved collaboration on biodiversity research projects.

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"How do I correctly use names and know which one is valid?"

4 Nomenclatural Resources

Knowledge and training in nomenclature is extremely important for systematists. A little bit of Latin helps but also understanding the International Code of Botanical Nomenclature can make life easier.


International Code of Botanical Nomenclature online (ICBN): http://ibot.sav.sk/icbn/main.htm
      The ICBN establishes rules for botanical nomenclature and is the best resource for understanding the nomenclatural system for plants and lichen.

Global Names Initiative (GNI): http://www.globalnames.org/
      A website that helps you to find information about biological groups across all domains of life through a search system that leads the user to other web resources. Under the find names service, the system detects scientific names in documents, URLs or any type of free text. This service is very useful for finding names in encrypted or image-based PDFs.

The Plant List: http://www.theplantlist.org/
      The Plant List began in 2010 and was updated in 2013 as a global effort to store and make available all known names of vascular plants and bryophytes. It aims to be the most comprehensive global list of plant taxonomic names.

Taxonomic Name Resolution Service (TNRS): http://tnrs.iplantcollaborative.org/index
      TNRS is an application that can be used to confirm taxonomic names. Large lists (up to 5000 names) can be submitted to confirm identities and names and you can select multiple databases to check whether a name is correct and by what authority.

Index Fungorum: http://www.speciesfungorum.org/
      Index Fungorum is the main nomenclatural database for fungi (including lichens) with over 380,000 names. It provides reliable information on currently used names and its synonyms.

Integrated Taxonomic Information System (ITIS): http://www.itis.gov/index.html
      ITIS has information on the taxonomy and nomenclature of the searched taxon as well as information about the taxonomic hierarchy. It also provides the user with a list of experts in the taxon and links where one can find information about a given organism.

International Plant Names Index (IPNI): http://www.ipni.org/
      The International Plant Names Index (IPNI) is a searchable database containing information on plant nomenclature, authorities, and author publications. IPNI is an excellent resource for looking up plant names and authors. Nomenclatural data comes from the Index Kewensis database, supported by the Kew Botanical Gardens.

Mycobank: http://www.mycobank.org/
      Mycobank is a fungal nomenclature and species bank. When describing a new species, journals are requiring the authors to include a Mycobank number that has information about the species, for example further description and additional photographs. It also ensures the author that the name chosen has the correct Latin declination and protects the name until it is validated by a peer reviewed journal.

Universal Biological Indexer and Organizer (Ubio): http://www.ubio.org/
      Another web-based nomenclatural tool, currently designed to integrate biological name data and classification data. The Name Server tool is described as a biological “name thesaurus”. Also contains introductory information on classification and species concepts.

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"Where can I find scientific vouchers for study? How to handle specimens appropriately?"

5 Collections and Collections Management

Herbaria serve as the primary collections-based institutions for plant and lichenological research internationally. Herbaria are located all over the world and are important and rich sources of material for systematics research. Below is a link to a searchable index of international herbaria, as well as some links to organizations which serve curators and provide resources for collections-based research (including preparation of specimens for both physical and digital preservation).


Biorepositories: http://www.biorepositories.org/
      Biorepositories is a database of natural history collections accession information. Biorepositories works with numerous institutions and will also be linking with other large collections databases in the near future, including Index Herbariorum (below).

Global Genome Biodiversity Network (GGBN): http://www.ggbn.org/ggbn_portal/
      GGBN is a worldwide network of institutions that partner for the preservation and storage of genomic material from natural history collections in biorepositories/biobanks. The GGBN web portal includes an interactive search tool to find genetic resources from taxa of interest and where they are deposited in GGBN partner institutions.

Consortium of North American Bryophyte Herbaria (CNABH): http://bryophyteportal.org/portal/index.php
      CNABH is a distributed network dedicated to integrate herbaria that carry bryophytes offering tools to locate voucher specimens as well as to provide image search and checklists curated by experts in the subject.

Consortium of North American Lichen Herbaria (CNALH): http://lichenportal.org/portal/index.php
      Created similarly to CNABH, but integrating lichen research tools. Both were initially created by the American Bryological and Lichenological Society, but currently they are maintained by other partners.

Index Herbariorum (IH): http://sciweb.nybg.org/science2/IndexHerbariorum.asp
      IH is a searchable database of all herbaria in the world. IH is scheduled for a merger with other searchable collections databases with biorepositories.org in 2012 and the URL and link is subject to change.

Integrated Digitized Biocollections (iDigBio): https://www.idigbio.org/
      iDigBio is an online resource for promoting the digitization of biological collections. This site facilitates digitization and makes digitized specimens available to the public.

International Society for Biocuration (ISB): http://www.biocurator.org
      Like SPNHC, ISB is a leading international organization for biocuration, and provides support of and advocacy for biocuration.

Society for the Preservation of Natural History Collections (SPNHC): http://www.spnhc.org/
      SPNHC is an international organization which promotes the curation, preservation, and innovation of natural history collections and provides resources for researchers interested in such collections.

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"I need to collect specimens, how do I do this legally?"

6 Fieldwork and Permitting

As a graduate student, you might need to collect your own material, which means you will most likely need a permit to do so. We acknowledge that different parks and states require different permitting processes; therefore, we encourage the user of this guide to look for specific laws that apply to the relevant jurisdiction. We have some suggestions to help to start the process.


Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES): http://www.cites.org/
      CITES is an international organization which governs importation and exportation of endangered species across international borders. CITES also helps facilitate communication of researchers who may be importing or exporting listed species, requiring a permit. National agencies charged with permitting can be found at: http://www.cites.org/cms/index.php/lang-en/component/cp/

United States Fish and Wildlife Service (FWS): http://www.fws.gov/ and http://www.fws.gov/permits/
      The USFWS provides permits for research activities in localities under USFWS jurisdiction. If you are uncertain whether your research requires permits, visit the link above or contact a FWS representative.

United States National Park Service (NPS): https://science.nature.nps.gov/research/ac/ResearchIndex
      The USNPS grants permits for collecting wildlife materials from locations within the US National Park system.

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"Where can I find information about protocols for a new or unfamiliar laboratory technique? Are there tools available online to help me troubleshoot my methods and protocols?"

7 Laboratory Protocols

Developing new lab protocols or troubleshooting existing protocols can often take more time than first expected. Searching for the right reference to troubleshoot can be difficult; however, there are some helpful techniques and resources available to pinpoint your problems. For many of these, there simply isn’t an alternative to a good textbook reference and we have listed some below; however, there are some web-based tools available to provide general support. There are two texts that are highly recommended for laboratory basics and troubleshooting: Barker (2005) and Hillis, Moritz and Mable (1996).


Lab Protocol: http://www.labprotocol.com/index.php
      Lab Protocol is a website aiming to help laboratories and researchers to look up protocols available from different institutions and to store their own methodologies for easy access. This resource has protocols in several areas of biology.

Protocol Online - Your lab’s reference book: http://www.protocol-online.org/
      Protocol online offers a variety of protocols related to biology in several subcategories. It also provides creative ideas for activities for teaching biology in different levels of education.

Promega, Inc.: http://www.promega.com/resources/
      Promega is a well-known distributor of molecular laboratory products and services. While most support offered online through Promega is specific to products they offer, they also offer some helpful information services free-of-charge through their resources page.

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"I need intensive or specialized training not available at my university"
"Where can I find lectures and other learning material online?"

8 Courses, Workshops, and Guides

Courses and workshops are an important part of graduate student training, but sometimes your university doesn’t offer everything you need. In this section, we include a list of courses in systematics-related fields that are offered annually by institutions with open registration to graduate students and professionals, alike. We also present a short list of guides for different programming and scripting languages. Each guide is written with a specific emphasis on biological applications or programming languages that are more often used by those in biological disciplines.


8a Online educational resources–
Codecademy: http://www.codecademy.com/
      Codecademy is a free training service available to anyone, which offers computer code teaching exercises for basic and advanced programming applications. Guided teaching modules allow users to familiarize themselves with basic scripting tools for writing their own applications and also developing their own website.

iTunes Podcasts on iTunes U: http://www.apple.com/education/itunes-u/
      iTunes U provides lecture and classroom content for download online. Material available through iTunes U is available through any device which can run iTunes software. Lectures can be recorded, uploaded, and stored on iTunes and made available to students or the general public. Photos and other multimedia documents can also be stored along with individualized notes that can be synchronized with the lecture. This is a free resource and several universities and colleges are already making lectures publicly available.

Udacity: http://www.udacity.com/
      Udacity provides free teaching modules for the public in basic and advanced computer programming applications. Udacity’s teaching modules are guided and application-based. All lessons can be completed within web-browser of choice.

BioPerl: http://www.bioperl.org/wiki/Main_Page
      The wiki available through BioPerl offers resources for training biologists in the use of Perl scripts for data analysis. Script templates for common tasks are available for download and the community at BioPerl is able to answer questions for users who encounter problems with data, datasets, or Perl scripts.

Lichen Web Pages at the Farlow Herbarium, Harvard University: http://www2.huh.harvard.edu/collections/lichens/
      This website hosts guides to several subjects in general or North American lichenology. It provides the user a vast list of literature about different topics when working with lichens in the US, but also tips on important characters of different morphotypes in lichens. Under the “How to collect lichens?” link, to advise people on how to collect lichens appropriately is the objective of this text developed by Philip F. May. The information available in the website contributes for a good quality material and analysis in depth.

8b In-person resources–
Bodega Phylogenetics: http://treethinkers.org/
      Bodega Phylogenetics hosts an annual Applied Phylogenetics Workshop each summer at the Bodega Marine Lab in Northern California. The Bodega Phylogenetics team also maintains and actively updates their Wiki page, where visitors can download tutorials and participate in discussions.

Evolution and Genomics (Evomics): http://evomics.org/
      Evomics offers workshops and training in molecular evolutionary biology and genomics. Tutorials and other resources are available through their website, above and several workshops are hosted internationally throughout the year.

Organization for Tropical Studies (OTS): http://www.ots.ac.cr/
      OTS is a non-profit organization created in a partnership between universities from the US, Australia and Latin American countries to promote tropical biology. It offers courses about different domains of life but also related to conservation of species and management of natural resources. Undergraduate and graduate courses are available year-round. It is a good opportunity for a hands-on experience in the tropics, since most courses are taught in Costa Rica.

Tropical Botany Course (University of Florida Department of Botany): http://www.flmnh.ufl.edu/herbarium/news/tropicalbotany.htm
      Each summer, Dr. Walter Judd teaches a course on tropical field botany through the University of Florida, Fairchild Tropical Botanical Garden, and The Kampong of the National Tropical Botanical Garden. Information about applications, registration, and fees are located at the link, above.

Woods Hole Marine Biological Laboratory (MBL): http://www.mbl.edu/
      MBL offers a suite of summer courses for students interested in intense training in specific areas. MBL provides some competitive scholarship opportunities for student attendance at the courses.

Molecular Evolution: http://www.molecularevolution.org/
      This resource brings several activities in a variety of software and molecular evolution concepts. It is a website encouraging the self-learning process by providing instructions and different files, so the students can download the software and have a hands-on experience in the internet.

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"Do I need money to do my research? Most likely yes!"

9 Funding

Funding is an important part of academic research and securing funds for research is a requirement for anyone who wishes to pursue research professionally. Graduate school is an excellent place to begin grant writing. Often, professional societies (see category, below) have small research grant awards available to graduate students. Other non-profit organizations, scientific foundations, and other institutions have larger awards available, which may include small grants or larger fellowships. Below are some links to groups which provide grant and fellowship opportunities for graduate research in the sciences, however, we encourage students to explore other sources of research grant awards, including professional societies they belong to and other non-profit organizations which support research in systematics and plant and lichen research.


American Philosophical Society (APS): http://www.amphilsoc.org/grants
      APS has provided grants in support of basic research since 1933. There are several grant opportunities available to students and early career scientists, which can be viewed through the link above.

National Science Foundation (NSF): http://www.nsf.gov/funding/
      Opportunities for students include predoctoral fellowships and doctoral dissertation improvement grants (DDIG).

Fulbright: http://us.fulbrightonline.org/
      The Fulbright student program has been active since 1946 and provides competitive research awards to students internationally, although the link above is for students who are U.S. citizens. Research awards include funding for residency in the country of study.

Garden Club of America (GCA): https://www.gcamerica.org/scholarships
      The GCA offers several grant awards in several plant-related research activities.

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"Is there a program that can do X, Y, or Z with my data already? Or do I have to write it myself?"
"I have a lot of intensive computational analyses to do, but not enough machines or time..."

10 Computing

Computational resources are increasingly important in systematics as a means of data storage and sharing, as well as distributing computationally intensive tasks onto remote processors. The systematics-based computing resources described in this paper have been categorized here largely as a distributed software resource and below we have listed cloud (i.e, distributed) computing as well as links to software resources. Cloud computing is entirely remote and this can be problematic for template files and software which can be prone to error from incorrect input. We suggest users new to cloud computing always prepare a “short” input file as a test, to make sure it is read properly by whatever remote software is being used. If possible, it may also be a good idea to try to run a short version of the input template on a computer at the user’s home institution before uploading it to the cloud. The best introduction to computing resources for systematists is to understand what tasks are required for your specific research and to review the available software. A list of tools available for phylogenetic research is listed below. We also recommend that users explore a scripting language to familiarize themselves with common notation and file formats. To assist systematists with this last recommendation, we have provided links to some useful language-related guides that are available for free over the web.


10a Software and Tools– There are thousands of software programs available for various types of phylogenetic data analysis. Many programs have been developed by researchers who have simply shared their code freely, others are available for purchase. The large amount of data generated by phylogenetics projects requires software that can organize and filter data, as well as compute summary statistics or analyze computationally intensive datasets. An important point to remember is that not all available programs are subject to rigorous or ongoing beta-testing and that their performance is not guaranteed.  Popular programs typically have community-based message boards, such as wikis, that may list important bugs or other limitations not otherwise described in the user-manual. One of the first steps is to download and become familiar with a good text editor program. We suggest TextWrangler (for Mac) or Notepad++ (for Windows).

Alignment Transformation EnviRonment (ALTER): http://sing.ei.uvigo.es/ALTER/
      ALTER is a web-tool which allows for fast and easy file format conversion. There are numerous file formats used by different software programs and you will inevitably need to perform file conversions if you are using phylogenetic software.

BLAST: Basic Local Alignment Search Tool (BLAST): http://blast.ncbi.nlm.nih.gov/Blast.cgi
      Blast is a useful program to find regions of similarity between sequences. It compares user-uploaded sequences and/or sequences already in the NCBI database (see above) and provides information about the potential identity of query sequence data, based on matches in the system. There are several versions of the program and they differ in the use of protein or nucleotide sequences.

Felsenstein’s UWash Program and Software List: http://evolution.genetics.washington.edu/phylip/software.serv.html#servers
      A list of currently active phylogenetic software and programs for all manner of applications in systematic biology. The list is maintained by the Felsenstein lab and developers can submit software to the host for addition of new packages and updates. Links to downloads and brief description of the software are provided. The user can search the packages by name, method, computer system, etc.

Text Wrangler: http://www.barebones.com/products/TextWrangler/
      Text Wrangler is a text editor that goes beyond the usual software. It offers more options in types of search, replacement, and editing overall and has an interface that can be used with Unix. It is free, but only available for Macintosh.

Another well-regarded source for biologists interested in a thorough introduction to computing is approached in Haddock and Dunn (2011). Unix and Python are some of the programming resources covered among other data analysis resources.

10b Cloud computing– Cloud computing allows users to both store data and operate computational tasks remotely. Remote storage and computing can be valuable for backing up data and also accomplishing tasks that often exceed the processing power or time available to researchers at their home institution. Many cloud resources are available for modest fees (and sometimes free!).

Amazon Web Services: http://www.aws.amazon.com/
      AWS offers low-cost storage and distributed computing services for a variety of tasks. Many users have developed computing pipelines for analyzing large (often genomic) datasets through AWS.

Cyber Infrastructure for Phylogenetic Research (CIPRes): http://www.phylo.org/index.php
      CIPRes Science Gateway is a web-portal for performing computationally intensive phylogenetic analyses for researchers with reduced computing capacity. It is a free service, but the user needs to create an account prior to send out analysis. An individual account can consume up to 30,000 CPU hours of computing time, or 50,000 for users affiliated with US institutions. With an account, one can manage several folders for parallel projects. It is very user friendly: Once a data file has been uploaded, that file can be analyzed using any of the appropriate tools available on CIPRes. It can take anywhere from a few minutes to several days for a job to complete. Plan ahead of time and ensure your file is formatted appropriately. CIPRes provides detailed instructions for file formatting and file testing before running a full task.

University of Oslo Bioportal: http://www.bioportal.uio.no/
      Web-based portal for phylogenetics and population genetics analysis. It is a host website for more than 40 programs, where the users can download programs to their computers as well as use it as a server. If used as a server, the bioportal of University of Oslo accesses a cloud space making it a good resource for time consuming computation. Similar to CIPRes in the types of analyses available.

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"Has someone else collected a dataset I could incorporate into my own research? Where can I archive and store my data, besides my lab notebooks, my hard drives, and my publications?"

11 Databases

Many databases exist for storing biological data generated by researchers around the world. These databases are often open access and freely accessible for use by other researchers with strict permission and use rules. Below, we have listed databases according to content, including molecular-based and phylogenetic-tree based databases. These databases are also frequently available for storing, uploading, and in some cases backing up your own data.


11a Molecular–
Barcode of Life Database (BOLD): http://www.barcodinglife.org/
      BOLD is a resource meant to promote and support the development of DNA barcodes for living organisms, internationally. BOLD serves as an international repository of DNA barcode data and a resource for information on barcodes.

NCBI Genbank: http://www.ncbi.nlm.nih.gov/
      Genbank is a web resource developed for the purpose of storing and maintaining molecular genetic data. Genbank is part of an international sequence database, which also includes sequence data from the DNA Databank of Japan (DDBJ), European Molecular Biology Laboratory (EMBL), and Genbank. Currently there are more than 100 million sequence records in Genbank, each of which is publicly searchable. Some search tools available through Genbank are described below.

11b Phylogenetic–
Dryad: http://datadryad.org/
      A repository of data governed by a consortium of journals that aims to facilitate the distribution of additional data from published peer-reviewed articles. Since most journals have limited space, Dryad offers an opportunity to the authors to deposit additional information and make it available online for further investigation and discussion. The submission of data is very user friendly, there is even a YouTube video available showing the process.

TREEBASE: http://treebase.org/treebase-web/home.html
      TREEBASE is a database available to researchers as a place to submit and store “phylogenetic trees and the data used to generate them”. Data stored on TREEBASE is linked to the publications that the data was originally published in for free communication of datasets and reproducibility.

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"Where can I find maps to use in presentations, publications, and analyses? GIS software is expensive and challenging to use, are there any tools that make this easier?"

12 Geographic Information Systems (GIS) and Maps

Geographic species distribution data is increasingly becoming a bigger part of molecular systematics studies. Understanding species distribution is critical for biogeographic analysis and species range or locality data can often be incorporated from collections housed in herbaria or other internet databases described in this document. A common problem for systematists who incorporate distribution data is finding useful and appropriate map resources.


12a GIS Data–
Federal Geographic Data Committee (FGDC): http://www.fgdc.gov/
      FGDC is a multi-agency host of geographic data, which provides maps and other resources as well as grants and training opportunities for researchers. FGDC is hosted by the USGS.

Natural Earth: http://www.naturalearthdata.com/
      Natural Earth is a host of open access, public domain map and GIS data. These high quality resources are freely accessible through the downloads section of the website and there is also a discussion forum and blog where users can discuss topics and ask questions.

WorldClim Global Climate Data: http://www.worldclim.org/
      WorldClim is a freely-accessible data repository for GIS climate and ecological data.

12b GIS tools–
Earth Explorer: http://earthexplorer.usgs.gov/
      The Earth Explorer web-tool is maintained and hosted by the US Geological Survey (USGS) and is a public repository that hosts searchable map and GIS data.

ESRI, Inc.: http://www.esri.com/
      ESRI, Inc. produces and sells the most used GIS software in the world, ArcGIS. In addition to developing this expansive software, ESRI provides GIS information and resources for users and hosts data (some of which is available for free through their website).

National Geographic Map Maker Interactive (MMI): http://education.nationalgeographic.com/education/mapping/interactive-map/?ar_a=1
      As the name implies, MMI is an interactive, web-based map making tool which employs a user-friendly Flash interface to scan, search, and select maps of geographic interest. Maps can be manipulated using the interactive web tool and downloaded to your computer. 

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"Are there organizations I can join that support my research,or offer assistance through networking and collaboration, funding, or other resources?"

13 Professional Societies

Below are several professional societies relevant for plant and lichen systematics researchers; some of which publish journals and offer affordable student membership rates. Professional societies can be an excellent way to meet potential collaborators and network with other researchers in your field of interest.


American Bryological and Lichenological Society (ABLS): http://www.abls.org/
American Fern Society (AFS): http://amerfernsoc.org/
American Society of Naturalists (ASN): http://www.asnamnat.org/
American Society of Plant Biologists (ASPB): http://my.aspb.org/
American Society of Plant Taxonomists (ASPT): http://www.aspt.net/
Botanical Society of America (BSA): http://www.botany.org/
Canadian Botanical Association/ L’Association Botanique du Canada (CBA/ABC): http://www.cba-abc.ca/cbahome.htm
International Association for Lichenology (IAL): http://www.lichenology.org/
International Association of Plant Taxonomists (IAPT): http://www.iapt-taxon.org/index_layer.php
The Mycological Society of America (MSA): http://www.msafungi.org/
Society for the Study of Evolution (SSE): http://www.evolutionsociety.org/
Society for Systematic Biology (SSB): http://www.systbiol.org/<

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"How can I find potential collaborators online or join a community of like-minded researchers?"

14 Social Networking

Electronic social networking applications are becoming more widely used by researchers for both traditional networking and also to share ideas and collaborate on projects. News and events can be disseminated, discussed, and tracked for a variety of purposes - we encourage readers to investigate some of the networking potential these resources offer.


Academia.edu: http://academia.edu/
      This site caters to students and researchers in academia, providing opportunities to “follow” the research of colleagues or other researchers whose work you might have an interest in. Academia.edu allows users to post links to manuscripts and can link users based on their discipline and academic interests.

Facebook: http://www.facebook.com
      More and more professional organizations, researchers, and funding institutions are networking and updating news and providing research announcements with tools available through traditional social networking sites, such as Facebook.

My-Plant: https://my-plant.org/
      My-Plant is a social network, hosted through the iPlant Collaborative (listed above). My-Plant provides networking and information using a tree-based phylogenetic approach. Researchers and collaborators can “join” a particular clade of interest and discuss research, news, and interact through the services available at My-Plant.org.

Twitter: https://twitter.com/
      Similarly to the networking possibilities available through Facebook, Twitter has also become a useful tool for interacting with potential collaborators, as well as following news and information from institutions, researchers, and professional societies.

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