The Submission Process The usual sequence of events is as follows: the author submits a paper for review and initiates a TreeBASE submission. At this stage, the submission is classified as "in progress" -- a submission number is issued (e.g. "SN345") so that the author can return to the submission at a later date and a P.I.N. is issued (e.g. "653453") so that a journal editor or referee can inspect the uploaded data. When the journal editor says that the paper is "accepted" or "accepted with minor revision," the author can return to the submission and change its status from "in progress" to "ready." At that point, TreeBASE staff will verify that the submission is complete, and if so, the data are made public and the study accession number (e.g. "S123") is generated and emailed to the author. Note that the submission number is not the same as the study accession number -- the former is only temporary, the latter is permanent. In addition, one or more matrix accession numbers are issued, each one specifying a specific data matrix. The author can, if he or she wishes, insert these numbers in the final draft of the manuscript or in the galley proofs. Authors submitting only one data matrix may wish to only report just the study accession number; authors submitting several matrices may wish to report the matrix accession numbers and indicate which one belongs to which dataset. Sometimes the author would like to have the data withheld until the journal issue has reached the library shelves. In such cases, the author should simply keep the submission status "in progress," and only change it to "ready" once the journal issue is published. However, this does not allow the author to include the final accession number in the paper. Authors who want to publish accession number and have the data withheld should email TreeBASE staff with specific instructions to this effect. The following requirements must be met for TreeBASE to accept a submission: The paper must be published in a peer-reviewed journal or book. Data for manuscripts that are "accepted with minor revision," "accepted," or "in press" can be included in TreeBASE. Data for manuscripts that are "submitted" or "in preparation" must not move beyond the initial stage of TreeBASE submission. The names of all authors listed with the paper must be included. At least one data matrix must be included. At least one tree must result from an analysis of one or more data matrices. In principle we do not accept matrices that were not analyzed to produce a tree; nor do we accept a tree for which the matrix used to produce it is missing. Normally the trees should be limited to those that were published as figures in the manuscript. However, a set of trees that were used to produce a published consensus tree is also acceptable (within reason). If a tree is not published in a figure but its existence is discussed in the text then it is also, in principle, acceptable. Only matrices and trees listed with an analysis will be included in the submission. A tree may be listed with only one analysis, but a matrix can be listed with more than one analysis. The Nexus Format The (unpaid) staff at TreeBASE will be grateful if (for the time being) you submit your data in nexus format, but we will happily accept your data in other formats as well. We plan on including automated data entry pages for PHYLIP and Hennig86 formats in the future, but for now we are only doing automated tree annotation for NEXUS files. We want to work with you to get your data into TreeBASE, regardless of format. If your data are not in nexus format, please email the data to us, and we will make the conversion for you. Otherwise, please proceed with the automated submission process (below). Things you will need: This web submission system will require that you copy and paste the abstract, and later, the nexus file, into "text areas." Some web browsers do not allow large files to be pasted into a field. For example Microsoft Explorer does not allow much more than 10 Kbytes to be pasted into a text area. In contrast, recent versions of Netscape do not appear to have this size limit. If you are submitting a large dataset, we suggest that you use Netscape. If you are submitting a dataset of more than 500 Kbytes, we recommend that you contact us and warn us in advance. You will need your name and email address. The reference to the publication (as best you can -- if the paper is "in press" omit the page numbers for now). The abstract . One nexus file for each matrix. Each nexus file must contain a data block and zero or more trees. In the case of an analysis on two or more datasets (e.g. one morphological and one molecular) these can be submitted as one combined nexus file, or (better yet) as two or more separate nexus files. If submitting separate nexus files, and if one tree resulted from the combined analysis, include this tree in either nexus file (but not both, or the tree will be added twice). Please do not include branch lengths in the tree file! (i.e., remove the colon notation and the values which are used to indicate branch lengths or bootstrap values). Each tree in the nexus files should be named according to the figure name in the publication (e.g. "Fig. 2"). Note whether each tree is a "single" tree (e.g. a single most parsimonious tree) or a "consensus" tree (the consensus of two or more trees). As a rule, we will accept up to 20 trees per submission. If your submission contains more than 20 trees, please contact TreeBASE staff for advice. Be prepared to provide names for internal nodes (i.e. higher taxonomic names). Be prepared to provide a summary of your phylogenetic analyses. Each analysis is applied to one or more matrices and results in one or more trees. You will be asked to identify each matrix and each corresponding tree. You will be asked to note the basic algorithm and software used. Please verify that taxonomic names are correctly written. If names need to be edited, delete the matrix and then resubmit an edited nexus file. Ideally, edit the nexus file in MacClade ahead of time so that names changed in the data matrix precisely match those in the trees. For taxonomic names: Avoid using abbreviations (e.g. write Homo_sapiens, not H._sapiens). Avoid brackets, parentheses, commas, colons, and semicolons. Use periods instead. Avoid using codes for non-redundant names (e.g. write Drosophila_melanogaster, not DMelan45GRX). However, it is acceptable two write Drosophila_melanogaster_45GRX if the same tree also contains other populations within the same species. Avoid using nonspecific names, such as Hypothetical_Ancestor, or Outgroup. Instead, write something specific, such as Outgroup_to_Magnoliaceae. Verify that taxon names found in trees are also found in all corresponding matrices. Remember that nexus format requires that you use a "_" instead of a white space (i.e.: " "), and any taxon name containing characters other than alphanumerics or period must be surrounded by single quotes, e.g.: 'Zygiella_x-notata'. Preview of the submission page. Our submission system does not require that the entire submission be completed in one sitting. In fact, it is designed to allow submitters to return, edit, and add to their submission at any time in the future until it is finally complete. In order to return to an incomplete submission, you need to remember your submission number. The following is an overview of what the submission page contains and what you need to do in each section. Section A. Enter the names of authors and their respective email addresses here. Use of first and middle names instead of first and middle initials will better help identify the author, especially if the last name is common (e.g. "Smith"). Click "Add Author" to accept the new author. Click "Delete Author" to remove the last listed author. Section B. Enter the reference here. If the article is "in press," you may not have page numbers available. If so, just enter as much information as you can. Later, send us an email with the complete reference. Avoid the use of strange characters. Click "Update" to accept the modified reference. Section C. Enter the abstract here. The program will remove return keys automatically. Click "Update" to accept the abstract. Section D. Click the "Add Matrix" button to submit a nexus file. If possible, please edit your nexus file with MacClade prior to posting it. This will improve the chances of successful parsing. After clicking "Add Matrix" you will be presented with the following page: Using copy/paste, enter the nexus file in the window and click the "Upload Data" button. After a short delay, you should see a page that looks like the following: From the popup list that appears that the top of the page, select the type of data that you are submitting (e.g. morphological, nucleic acid, etc.). Then name your matrix. If your matrix was published, please use the name of the table or appendix as it appears in the publication (e.g. "Table 2" or "Appendix A"). Otherwise, pick a suitable name (e.g. "Not printed" or "12S mtDNA"). This page summarizes the nexus data that you sent in, and therefore it is an opportunity to verify whether the data were parsed correctly. For example, if you submitted data with character labels and states, these should appear in blue text (character label names) and red text (character state names). If you don't see them, then the parser may have failed. Likewise, under "Data Synopsis" you should see a list of the taxa in the matrix (blue text) followed by the first 15 characters for each taxon (red text). If these data are missing then it's safe to conclude that your nexus file did not get parsed correctly. So what should you do if your nexus fails to parse properly? Try any of the following: Open your data in MacClade, than save it, and resubmit. Remove comments If you have large amounts of data in the Assumptions or Codons block, try removing them. Have MacClade save your data in an older nexus format If none of these succeed, email your data to us and we will try to figure out what is wrong. If your data appear to be parsed accurately, click the "Submit Data" button and you will return to the submission page. Whenever you upload data in this fashion, the submission page will reflect your additions in Sections E, F, and H. Section E. This section lists any matrices that have been uploaded. If you completed Section D, your matrix should be listed here. If you need to add a second (or third matrix, etc.), just click the "Add Matrix" button in Section D and paste in yet another nexus file. If you need to delete a previously entered matrix, select it from the popup menu and click the "Delete Matrix" button. Section F. This section lists any trees that were uploaded within nexus files entered in Section D. Here you are asked to name your trees as they appeared in the publication (e.g. "Fig. 2"), and assign your trees one of two basic categories: "single" for an individual tree resulting from an analysis (such as a most parsimonious tree, or a preferred tree from a selection of most parsimonious trees); "consensus" for a tree that is a consensus of two or more single trees. Finally, you are asked to provide a recognizable title for each tree (e.g. "Rosaceae" "angiosperms" "Primates" "Green Algae" etc.). Click the "Update Tree Data" button to save the changes that you made. By each tree is a button called "Edit Nodes." Please use this feature to name internal nodes (i.e. higher taxa). You should see something like the following: In the center of the page, you should notice a graphic representation of the tree. If you move your mouse over the branches of the tree, you should see a message flicker in the message window (see the red arrow in the figure on the left -- it is pointing to the message window). This message gives the sequence number for a particular node, as well as it's name if it has already been named. Nodes that are already named are given a red dot (see the branch that the mouse is pointing to on the left) and they are listed separately below the tree. To name a node, simply click on the appropriate branch, enter a name in the field, and click the "Enter Node" button. You will return to the page displaying the tree, but now you should see a red dot beside the branch that you had just edited. Additionally, the name should be listed separately below the tree. Why name nodes? Attaching a name to a branch or node allows users to more easily find your tree and provides better connectivity between trees. For example, supposing users are not familiar with the specific, binomial names for trees in the genus Acer. It would be helpful, therefore, to name the basal branch "Acer" for a tree containing Acer species. That way a search on the name "Acer" will find this tree without having to specify, for example, Acer japonicum. Continue clicking and naming as many nodes as you wish. When you're done, click the button at the bottom of the page to return to the submission page. Section G. In this section, you are asked to enter a basic outline of the analyses used to generate the trees in your study. In TreeBASE, analyses are the basic link between matrices and trees, so you must describe at least one analysis. Given the large diversity of phylogenetic methods available, TreeBASE cannot possibly store descriptions of all procedures performed by all authors. Weighting schemes, likelihood models, transformation matrices (etc.) go above and beyond the scope of TreeBASE. (However, retaining the notation for these features in the uploaded nexus file(s) will allow users to recover this information following a matrix download). TreeBASE does, however, seek to store a very basic overview of the data analysis used to generate the phylogenetic results of a study. A study can contain any number of analyses. Each analysis uses an algorithm (e.g. parsimony) with a software package (e.g. PAUP) on one matrix or on a combination of two or more matrices, leading to one or more trees. Take, for example, a phylogenetic study involving morphological characters and 12S mitochondrial DNA characters. Lets say that the authors presented five trees in their study: tree 1 results from a parsimony analysis on the 12S data alone; tree 2, a maximum likelihood analysis on 12S data alone; tree 3, a parsimony analysis on the morphological data alone; tree 4, a consensus of the five most parsimonious trees from an analysis of 12S and morphological characters together; tree 5 is a "preferred" tree, selected from one of the five most parsimonious trees. For purposes of TreeBASE, the authors might consider entering four analyses: three analyses using parsimony, of which one uses both matrices and results in two trees (4 and 5); and one analysis using maximum likelihood on the molecular data alone (tree 2). By clicking on the "Add Analysis" button, you will be presented with a page that lets you select which matrices go with which trees. This page lets you describe the relationship in terms of algorithm and software used. Section H. In this section, all taxa entered thus far (via nexus uploads) are listed. For each taxon, one or more matrix names follow. These indicate which taxa belong to which matrices This is your chance to verify that the names you have entered comply with our guidelines (see above under "For taxonomic names:"). It is also your chance to verify that the same taxon entered via two or more nexus files had an identical spelling across all nexus files. If any taxonomic names fail to comply with our guidelines, of if they appear misspelled (or differently spelled) in one or more matrices, please delete the corresponding matrix (Section E), edit the nexus file, and resubmit (Section D). Section I. This is the last section of the submission page. Here, you are asked to either save your submission "in progress" so that you can return to it later, or upload it for submission to TreeBASE. If you decide to save it so as to return to it later (for example, you decided to change the names of taxa, and get back to the submission process the following day) be sure to note down your submission number. That way you can return to where you left off at a later date. For security reasons, please use the same computer (i.e. with the same IP address) when you return to continue editing a submission. If you are using a computer which receives a temporary IP number (such as a PPP or slip connection) please finish your entire submission in a single session. A final word. This is a test version of TreeBASE; it is still very much under construction. The data submission form is new code and it doubtlessly still contains bugs. If you have difficulties with the form, please let us know. If you are ready to submit data, click here.