User Manual for Dendroscope V2.7.4
Contents
1. The Message window is opened using the Window gt Message Window item The program writes all internal messages to this window The window contains the usual File and Edit menu items 6 4 Export Image Dialog The Export Image dialog is opened using the File gt Export Image item This dialog is used to save an image of the current tree in a number of different formats see Section 8 5 The format is chosen from a menu There are two radio buttons Save whole image to save the whole image and Save visible region to save only the part of the image that is currently visible in the main viewer If the chosen format is EPS then selecting the Convert text to graphics check box will request the program to render all text as graphics rather than fonts Pressing the apply button will open a standard file save dialog to determine where to save the graphics file 6 5 About Window The About Window is opened using the Window About submenu Dendroscope About in MacOS It reports the version of the program and its authors 13 7 Additional Features 7 1 Using the Mouse to Select Nodes edges and labels can also be selected by clicking on them shift clicking to extend a selection or by shift dragging the mouse to perform rubber band selection in which all objects contained within a dragged rectangle are selected 7 2 Magnifier Functionality Dendroscope provides the user with a magnifier functionality that can be used to magnify p2. It is time for a stan dard representation 2008 Submitted to BMCB http bioinfo uib es media uploaded bmc 2008 enewick sub pdf 2 Daniel H Huson Splitstree analyzing and visualizing evolutionary data BIO 14 1 68 73 1998 http bioweb pasteur fr docs doc gensoft splitstree splitstree ps 3 Daniel H Huson Drawing rooted phylogenetic networks TCBB 2008 To appear 4 Daniel H Huson Tobias Dezulian Markus Franz Christian Rausch Daniel C Richter and Regula Rupp Dendroscope an interactive tree drawer BMCB 8 460 2007 http dx doi org 10 1186 1471 2105 8 460 software freely available from http www ab informatik uni tuebingen de software dendroscope 19 Fa SunflowersA_55 nexus 2 Dendroscope E iol x File Edit Select Option View Window Baai i 3200 HP MEN QEE lt LAGOHOS M m Nicotiana Campanula Scaevola Stokesia Dimorphotheca Senecio Gerbera PA Format SunflowersA_55 nexus 2 Dendroscope io x Gazania File Edit Echinops Felicia z 10 y Bold Italic Tagetes Chromolaena ca TT Blennosperma Coreopsis Vernonia Cacosmia Cichorium Achillea Node Size 2 v Carthamnus Node Shape none Flaveria Piptocarpa Edge Width Helianthus Labels Rotate Left Tragopogon Chrysanthemum H Eupatoriu
3. Select Spanned Edges 6 Select Select Special 7 Select Select Subtree 6 selection 14 Set Window Size 10 shift click selection 14 Show Edge Labels 9 Show Edge Weights 9 Show Node Labels 9 show hide labels 12 Radial Labels 9 Recent Files 4 5 Regular Expression 12 Remove 11 Rename 11 Reorder Subtrees 6 Reposition Labels 9 Reroot 5 10 Respect Case 12 rooted network consensus 8 rotate labels 12 Rotate Left 10 Rotate Right 10 Rotate Subtrees 6 f Side Bar 11 a Sidebar gt Clear Formatting 11 Save 5 Sidebar gt Copy 11 Save As 4 5 10 Sidebar gt Duplicate 11 Save Font As Default 12 Sidebar Remove 11 Save visible region 13 Sidebar Rename 11 Save whole image 13 softwired representation 8 Scroll to Selection 7 Sparse Labels 9 Select 6 square nodes 12 Select All 6 Status Line 11 Select Edges 6 straight edges 12 Select Induced Tree 6 Strict Consensus 7 11 Select Labeled Nodes 6 strict consensus 7 Select Leaves 6 SVG 16 Select Nodes 6 Swap Subtree 10 Select Non Terminal 7 Swap Subtrees 6 Select Root 6 Select Spanned Edges 6 Toolbar 10 Tree 8 Select Special 7 Select Subtree 6 Select Deselect All 6 Select Deselect Edges 6 Select Deselect Nodes 6 Select From Previous Window 6 Select Invert Selection 7 Select gt List Selected Taxa 7 Tree Draw Circular Cladogram 4 8 10 Tree Draw Circular Phylogram 4 8 10 Tree gt Draw Intern
4. Sele Sele Sele Sele Sele Sele Inve Dese Dese Dese List ct all edges ct all labeled nodes as in previous window ct all labeled nodes ct all leaves ct all nodes in subtrees below selected ct part of subtree ct all non terminal nodes ct all intermediate nodes ct root ct all special edges rt the current selection lect all nodes and edges lect all nodes lect all edges all currently selected taxa find searchtext text target Nodes Edges all bool regex bool wholeword bool respectcase bool Find and select the next label matching the given search text replace searchtext text replacetext text target Nodes Edges all bool Collapsing and uncollapsing nodes collapse all collapse selection collapse complement collapse level number uncollapse all uncollapse selection uncollapse subtree Visualization Coll Coll Coll Coll Unco Unco Unco regex bool wholeword bool respectcase bool apse all nodes apse all selected nodes apse the complement of all selected nodes apse all nodes at the given level distance from root llapse all nodes llapse all selected nodes llapse whole subtree for selected nodes set window width num height num x num y num set font name set autolayoutlabels bool Set Set Set size and location of main window font by name auto layout of labels set margin left num right num top num bottom num show approxthreshold int sho
5. be available as Java Webstart application from www ab2 informatik uni tuebingen de webstart dendroscope If you need information concerning Java Webstart go to http java sun com products javawebstart 4 Getting Started This section describes how to get started and to do the first steps of analyses using Dendroscope First download an installer for the program from www dendroscope org see Section 3 for details Start the program and load any tre nexus or dendro project file via File gt gt 0pen Alternatively if the file was recently opened by the program then it may be contained in the File Recent Files submenu At startup the tree will be scaled to fit to the window size Draw the tree differently by choosing one of the 8 provided views e g Tree Draw Rectangular Phylogram Tree Draw Rectangular Cladogram Tree Draw Slanted Cladogram Tree Draw Circular Phylogram Tree gt Draw Circular Cladogram Tree Draw Internal Circular Cladogram Tree gt Draw Radial Phylogram Tree Draw Radial Cladogram Try out the magnifier functions by clicking on View Use Magnifier Change any label font size color or edge node size width by opening the Format Panel via Edit Format If you want to print the current image choose File gt Print In case you need a quality image of the tree simply export it to several file formats via File gt Export Image Finally if you want to save the tree s and the fo
6. graphics formats see Section 8 5 The File gt Print item is used to print the current tree The File gt Close item closes the current window In case only one window is opened the application exits The File gt Quit item quits the program Under MacOS _ this item is contained in the Dendroscope menu Edit Menu Edit menu contains the usual edit related items The Edit gt Copy item is used to copy the current tree or all selected trees The Edit gt Paste item is used to paste the copied trees to a new tab The Edit gt Find Replace item opens the Find window which can be used to search for taxa and labels The Edit gt Find Again item finds the next occurrence of a search string The Edit Reroot item reroots the tree at the specified node or edge If more than node is selected all selected taxon labels are intepreted as outgroup taxa and the program determines the tightest rooting so that the outgroup appear together below the root 5 3 The The Edit gt Swap Subtrees item swaps the subtree or subtrees at the specified node or nodes see also Section 7 3 The Edit Rotate Subtrees item rotates the subtree s at the specified node s The Edit Reorder Subtrees item opens a dialog that allows one to specific any type of reordering of the children of a node using drag and drop The Edit Delete Taxa item removes the selected subtree form the current tree The Edit gt Unlock Edge Lengths
7. is used to make edge labels visible The View Hide Edge Labels item is used to hide edge labels The View gt Sparse Labels item instructs the program to show only a subset of the taxon labels thus avoiding overlapping labels The View Radial Labels item instructs the program to rotate leaf labels to match the orientation of the edges that lead to them The View Reposition Labels item sets all the labels to their original position Window Menu The Window menu contains a number of window related commands as well as a list of all currently open windows The Window gt About item opens a splash screen showing the program version In MacOS this can be found under Dendroscope About e The Window How to Cite item shows the citation info for this software which is Daniel H Huson Daniel C Richter Christian Rausch Tobias Dezulian Markus Franz and Regula Rupp Dendroscope An interactive viewer for large phylogenetic trees BMC Bioin formatics 8 460 2007 e The Window gt Set Window Size item is used to set the size of the Main window e The Window Command line Syntax item lists all commands supported by the program e The Window Execute Command item opens a window that can be used to enter a command see command e The Window Add Tree or Network item opens a window to enter tree or network manually in Newick Format e The Window Message Window item is used to open the Message window e If several program windo
8. item is used to unlock edge lengths so that the user is allowed to move individual nodes and internal edge points The Edit gt Format item opens a Format Panel which provides several possibilities to change color fonts node and edge shapes and the positioning of the labels of the tree Select Menu Select menu contains items for selecting different sets of substructures of the tree The Select Select All item is used to select all nodes edges and labels The Select gt Select Nodes item is used to select all nodes The Select Select Edges item is used to select all edges The Select From Previous Window item is used to apply the selection of the previous window to the active window The Select gt Deselect All item is used to deselect all nodes edges and labels that are currently selected The Select gt Deselect Nodes item is used to deselect all nodes that are currently selected The Select gt Deselect Edges item is used to deselect all edges that are currently selected The Select gt Select Labeled Nodes item is used to select all labeled nodes The Select gt Select Leaves item is used to select all leaves The Select gt Select Subtree item is used to select the subtree below a selected inner node The Select gt Select Induced Tree item is used to select a subtree induced by the set of currently selected nodes The Select gt Select Spanned Edges item is used to select all edges spanned by the set of
9. subtree starting from this node A right mouse click on an edge opens a context menu which allows to edit the edge label open the Format Panel show or hide edge labels and copy the edge label A right mouse click beside the tree opens a context menu which allows to select or deselect all edges nodes and labels 5 10 Side Bar The Side Bar on the left contains a list of all trees in the current file The arrows on top can be used to browse the list Additionally one can change the order of the list by dragging and dropping single trees to a new position in the list The sidebar can be made in visible when clicking the small left right arrow located on the sidebar itself Right clicking on one of the trees listed in the sidebar opens a popup menu with the following items e The Copy item can be used to copy a tree e The Remove item can be used to remove a tree for the list of trees e The Rename item can be used to rename a tree e The Duplicate item can be used to duplicate a tree e The Clear Formatting item can be used to clear all formating of a tree such as choice of colors and fonts etc 5 11 Consensus Bar The Consensus Bar allows direct access to the following menu items e The Options gt Strict Consensus item e The Options gt Loose Consensus item e The Options gt Majority Consensus item e The Options gt LSA Consensus item e The Options Network Consensus item 5 12 Status Line The Status Line at
10. the bottom of the program window shows the index of the current tree the total number of trees the number of nodes and edges and the available space of the reserved memory 11 6 Additional Windows 6 1 Format Panel The Format Panel can be opened via Edit gt Format or by a right mouse click after selecting elements of the tree like edges nodes or labels You can format them as follows e Edges can have their edge width and edge width set Edges can be assigned three types of shapes straight edges curved edges and angular edges the effect of which depends on the current view Nodes can be assigned certain shapes square nodes circle nodes or none Square and circle node shapes They can have their node size and node color set If a selected node or edge has a label then you can choose its font family font style or font size Labels can be switched on and off and can be rotated to the left or right Configuration changes are applied immediately The Options Save Font As Default menu item can be used to set the default font style and size used by the program 6 2 Find Window The Find window can be opened using the Edit gt Find Replace item Its purpose is to find and also to replace taxa labels in the tree Enter a query specifying the name of a taxon in the top text region Use the following check boxes to configure the search e Ifthe Match Whole item is selected then only taxa or labels matching the comp
11. 4 8 10 Duplicate 5 11 edge labels 9 edge weights 9 edge width 12 Edit 5 Edit Copy 5 Edit Delete Taxa 6 Edit gt Find 10 Edit gt Find Again 5 Edit gt Find Replace 5 12 Edit Format 4 6 10 12 Edit Paste 5 Edit Reorder Subtrees 6 Edit Reroot 5 10 Edit Rotate Subtrees 6 Edit Swap Subtree 10 Edit Swap Subtrees 6 Edit Unlock Edge Lengths 6 Enter Command 16 EPS 13 16 exact method 8 Execute Command 10 Expand view horizontally 10 Expand view vertically 10 Export 4 5 Export Image 4 5 10 13 Extended Newick 15 Extract Subtree 7 File 5 File gt Close 5 File gt Duplicate 5 File gt Export 4 5 File gt Export Image 4 5 10 13 File gt New 5 File gt 0pen 4 5 10 File gt Print 4 5 10 File gt Quit 5 File gt Recent Files 4 5 File gt Save 5 File gt Save As 4 5 10 Find 10 12 MacOS 4 5 Find Again 5 magnifier band 14 Find All 12 13 magnifier functionality 14 Find First 12 Magnify All Mode 9 Find Next 12 Main 4 Find Replace 5 12 Majority Consensus 7 11 finding taxa from a file 12 majority consensus 7 font family 12 Match Whole 12 font size 12 Message 13 font style 12 Message Window 10 13 Format 4 6 10 12 minimum network 8 Format Panel 12 MRJAdapter 18 From File 12 From Previous Window 6 Navigating trees 14 Fully Contract 9 10 Network Consensus 8 11 Fully Expand 9 10 Network for Multi Label
12. 9 The Options Network for Multi Labeled Tree menu item is used to compute a rooted phylogenetic network for a multi labeled tree such that the network contains each label or taxon exactly once There are three methods available here the Cluster method extracts all the clusters in the tree and constructs a cluster network The exact method computes the nested label for the root node of the tree and then constructs the corresponding network for that label see Huber Oxelman Lott and Moulton 2006 The LevelK method extracts all clusters and then seeks to compute a level k network of minimum level k for the clusters Note that Dendroscope does not require that the trees all contain exactly the same set of taxa to be able to compute a consensus unlike most other programs 5 5 The Tree Menu Tree menu contains items for different tree and network views 3 The Tree Draw Rectangular Phylogram item is used to draw the tree as rectangular phylogram The Tree Draw Rectangular Cladogram item is used to draw the tree as rectangular cladogram The Tree Draw Slanted Cladogram item is used to draw the tree as slanted cladogram The Tree gt Draw Circular Phylogram item is used to draw the tree as circular phylogram The Tree gt Draw Circular Cladogram item is used to draw the tree as circular cladogram The Tree Draw Internal Circular Cladogram item is used to draw the tree as circular cladogram with leaves on the inside Th
13. Gorilla_gorilla_gorilla Gorilla_gorilla_graueri E orita goritauetenss Gorilla_gorilla_diehli E Pan_paniscus Pan_troglodytes_schweinfurthii TE Pan_troglodytes_troglodytes E Pan_troglodytes_verus L Pan_troglodytes_vellerosus git Homo_sapiens_neanderthalensis p Pongo_sp_ i r Pongo_pygmaeus_abelii E Pongo_pygmaeus_pygmaeus y Japanese_monkeys se marmosets L unidentified_monkey r Cynocephalus_variegatus Nodes 326289 Edges 326288 339 of 414M File Edit Select Option View Window BaS i 700 4d SM QEECKGKSGS A Ateles paniscus a eles fusciceps Ateles Callicebus_ slanacophs donacophilus Pithecia_pithec Cercopithecus_ as grayi Macaca_speciosa Hylobates_moloch Co Gorilla_gorilla_beringei Pag Pan paniscus Pan_troglodytes_verus E Pan_troglodytes_vellerosus Homo_sapiens_neanderthalensis Homo sapiens Homo_sapiens 1 M Pongo_sp_ ngo_pygmaeus_abelii panese_monkeys mocephalus_s variegatus Ochotona_erythrotis ii re Marmota_olympus Spermophilus_atricapillus Spermophilus_washingtoni Spermophilus_parryii_lyratus X gt Nodes 326289 Edges 326288 296 of 414M Figure 2 Part of the NCBI taxonomy showing Homo sapiens and his relatives without and with the magnifier turned on References 1 Gabriel Cardona Francesc Rossell and Gabriel Valiente Extended newick
14. User Manual for Dendroscope V2 7 4 Daniel H Huson Daniel C Richter Christian Rausch and Regula Rupp June 23 2010 Dendroscope by Daniel H Huson with contributions from Tobias Dezulian Markus Franz Christian Rausch Daniel C Richter and Regula Rupp www ab informatik uni tuebingen de software dendroscope Contents Contents 1 Introduction 2 Program Overview 3 Obtaining and Installing the Program 4 Getting Started 5 Main Window eel Ple MGD asar Se eek ee See Rew ee ee e Geo DAR Mamie sad a Bb ee Pe he eae ee a ee ae Ye a 3a pelee MENU o oa cde bee keen he keen d eee Gee ee ee Ewe ees 54 Options Meno 8404 04 5 a debe ee ala bY ae Ee ba eas is e Co fg hoe oR cee E ae ect a a Be A E 56 View Men s seces ceca ea Ad we ES ER ee we dae ee a e 5 7 Window Menu 5 8 Toolbar 5 9 Context Menus 5 10 Side Bar 5 11 Consensus Bar 5 12 Status Line 6 Additional Windows bl Format Pane cis is eh ee ee eS ee eo ee ae eee a Be Find Window e chee bee ke ended ewan d Pee Ges ee de ee Re eee G 63 Message WIMdOw casonas A de RE eee ek E A 6 Export maso Dialog ee o maed vo ee ee e dae a GS Aboni Widow lt lt 26 cueros asada da ede REE AG es 7 Additional Features T Using the Mouse to Select re ss de naaa eR ee ee 7 2 Magnier Functionslity 2 2 4 54 46 be Seek Ge Bae Re ee was 7 3 Navigating trees with keys and mouse wheel 00000 ee eae 8 File Formats 8 1 Dendroscope Files A He
15. al Circular Cladogram 4 8 10 Tree gt Draw Radial Cladogram 4 8 10 Tree gt Draw Radial Phylogram 4 8 10 Tree gt Draw Rectangular Cladogram 4 8 10 Tree gt Draw Rectangular Phylogram 4 8 10 23 Tree Draw Slanted Cladogram 4 8 10 Tree gt Ladderize Left 9 10 Tree gt Ladderize Random 9 10 Tree Ladderize Right 9 10 Tree gt Next Tree 8 Tree Previous Tree 8 Type setting conventions 3 Uncollapse 7 Uncollapse Subtree 7 Unix 4 Unlock Edge Lengths 6 Use Magnifier 4 9 10 14 View Fully Contract 9 10 View gt Fully Expand 9 10 View Hide Edge Labels 9 View Hide Node Labels 9 View Magnify All Mode 9 View Radial Labels 9 View Reposition Labels 9 View Show Edge Labels 9 View Show Edge Weights 9 View Show Node Labels 9 View Sparse Labels 9 View Use Magnifier 4 9 10 14 View Zoom to Fit 9 10 Views 9 Webstart application 4 Window 9 Window About 9 13 Window gt Add Tree or Network 10 Window Command line Syntax 10 Window gt Enter Command 16 Window Execute Command 10 Window How to Cite 10 Window Message Window 10 13 Window Set Window Size 10 Windows 4 Zoom to Fit 9 10 24
16. currently selected nodes The Select gt Select Root item is used to select the root node of the tree 5 4 The The Select gt Select Non Terminal item is used to select all non terminal nodes and edges The Select Select Special item is used to select all edges leading to reticulation nodes in networks The Select Invert Selection item is used to invert the current selection The Select gt Scroll to Selection item is used to scroll to the current selection The Select gt List Selected Taxa item is used to list all selected taxa Options Menu Options menu contains items for collapsing nodes and extracting subtrees The Options Collapse item enables to collapse a subtree at a selected specified node The former subtree is replaced by a new edge with label The Options Uncollapse item is used to uncollapse expand a selected collapsed subtree The Options Uncollapse Subtree item is used to uncollapse expand all collapsed subtrees of a selected node The Options Collapse Complement item is used to collapse all subtrees except the currently selected part of the tree The Options Collapse at Level item is used to collapse all subtrees at the specified level from the root The Options Extract Subtree item is used to extract a selected subtree to a new file The Options gt Load Taxon Images item is used to specify a directory containing image files Dendroscope tries to match taxon names to
17. e Tree Draw Radial Phylogram item is used to draw the tree as radial phylogram The Tree Draw Radial Cladogram item is used to draw the tree as radial cladogram The Tree gt Previous Tree item is used to switch to the last opened tree The Tree gt Next Tree item is used to switch to the next opened tree 5 6 The e The Tree Ladderize Left item is used to order the tree so that the largest clades appear leftmost uppermost in the view e The Tree Ladderize Right item is used to order the tree so that the largest clades appear rightmost lowermost in the view e The Tree gt Ladderize Random item is used to order the clades randomly View Menu Views menu contains items for scaling the tree using the magnifier and showing hiding labels 5 7 The View gt Zoom to Fit item is used to scale the tree to fit the window The View gt Fully Contract item is used to contract the tree The View Fully Expand item is used to expand the whole tree The View gt Use Magnifier item is used to turn the magnifier functionality on and off The View gt Magnify All Mode item modifiers the magnification process so that the whole tree gets mapped into the magnifier The View Show Node Labels item is used to make all node labels visible The View gt Hide Node Labels item is used to hide all node labels The View gt Show Edge Weights item is used to make edge weights visible The View gt Show Edge Labels item
18. e cg a eh a Oe eA Re ee a Se ee ee eee a eee haas So Newick files cocos 24 wee a DE HEE G EEG Eee Ee ee aS 8 4 Extended Newick format and rooted phylogenetic networks 8 5 Graphics Formats 9 Commands 10 Examples 11 Acknowledgements References 12 12 12 13 13 13 14 14 14 14 14 15 15 15 15 15 16 18 18 19 1 Introduction Disclaimer This software is provided AS IS without warranty of any kind This is develop mental code and we make no pretension as to it being bug free and totally reliable Use at your own risk We will accept no liability for any damages incurred through the use of this software Use of the Dendroscope is free however the program is not open source Type setting conventions In this manual we use e g Edit gt Find to indicate the Find menu item in the Edit menu How to cite If you publish results obtained in part by using Dendroscope then we require that you acknowledge this by citing the program as follows e Daniel H Huson Daniel C Richter Christian Rausch Tobias Dezulian Markus Franz and Regula Rupp Dendroscope An interactive viewer for large phylogenetic trees BMC Bioin formatics 8 460 2007 software freely available from www dendroscope org 4 2 Program Overview Dendroscope is a platform independent software written in Java that enables conveniently to browse phylogenetic trees and networks with up to hundreds of thousands of taxa Here is an ove
19. ed Tree 8 New 5 galled network 8 Next Tree 8 GIF 16 Nexus trees block 15 graphics formats 15 node color 12 node shapes 12 hardwired representation 8 node size 12 Hide Edge Labels 9 Hide Node Labels 9 Open 4 5 10 How to Cite 10 Open File 5 How to cite 3 Options 7 Options Collapse 7 Image Position 7 Options Collapse at Level 7 Image Size 7 Options Collapse Complement 7 Invert Selection 7 Options Extract Subtree 7 JPEG 16 Options Image Position 7 Options gt Image Size 7 key bindings 14 Options Load Taxon Images 7 Options Loose Consensus 7 11 Ladderize Left 9 10 Options gt LSA Consensus 8 11 Ladderize Random 9 10 Options gt Majority Consensus 7 11 Ladderize Right 9 10 Options Network Consensus 8 11 level 8 Options Network for Multi Labeled Tree 8 LevelK 8 Options gt Save Font As Default 12 Linux 4 Options Strict Consensus 7 11 List Selected Taxa 7 Options Uncollapse 7 Load Taxon Images 7 Options Uncollapse Subtree 7 Loose Consensus 7 11 outgroup 5 loose consensus 7 LSA Consensus 8 11 Paste 5 LSA consensus 8 PDF 16 22 PNG 16 Select Scroll to Selection 7 Previous Tree 8 Select Select All 6 Print 4 5 10 Select Select Edges 6 Select Select Induced Tree 6 Quit 5 Select gt Select Labeled Nodes 6 Select Select Leaves 6 Select Select Nodes 6 Select gt Select Non Terminal 7 Select Select Root 6 Select
20. el button and two two different apply buttons The Apply button applies the entered command to the current tree whereas the Apply to All button applies the entered command to all trees in the current file Here is a summary of all available commands Opening and saving files open file name init command Open the named file in the current window if empty otherwise in a new window and then optionally perform specified initial commands in new window launch file name Open the named file in the current window save format value file name Save data to file in the specified format possible formats nexus newick dendro exportgraphics format EPS PNG GIF JPG SVG PDF replace bool textasshapes bool title title file filename Export a picture of the current tree source file name Read commands from the named file Choosing tree and visualization set which value Sets the current tree possible values number of tree first last previous next set drawer drawer name Set the drawer used to draw the tree Possible values RectangularPhylogram RectangularCladogram SlantedCladogram RadialPhylogram RadialCladogram CircularPhylogram CircularCladogram InnerCircularCladogram set auxilaryparameter number Set the auxilary parameter used by some of the drawers Customizing the layout of a tree reroot Reroot current tree using currently selected set of nodes outgroups node or edge ladderize value Ladderize each displayed tree p
21. end of node labels These special labels are of the form HT 4H2 etc When parsing an extended Newick string all nodes whose labels end on H1 are identified with each other all nodes that end on H2 are identified etc For example to describe a rooted phylogenetic network with three leaves labeled a b and c in which b is to have a reticulate parent node that connects both above a and above c use the following extended Newick string Ca ob H1 c H1 Copy and paste this string into a Dendroscope window to see the corresponding network In Dendroscope anything that can be done with a rooted tree can also be done with a rooted phylogenetic network 8 5 Graphics Formats The following graphics formats are supported how to open the Export Image dialog see 6 4 15 e JPEG Joint Photographic Experts Group e GIF Graphics Interchange Format e EPS Encapsulated PostScript e SVG Scalable Vector Graphics e PNG Portable Network Graphics e BMP Bitmap e PDF Portable Document Format 9 Commands The program provides a command intepreter to access all its functionalities a command can be entered either using the Window Enter Command item or by starting the program in command line mode and typing or piping commands to the program via the console The Command window has a field for entering commands a canc
22. lete query string will be returned e Ifthe Respect Case item is selected then the case of letters is distinguished in comparisons e If the Regular Expression item is selected the query is interpreted as a Java regular expression see example further down If a searched label is hidden inside a bounding box black opaque area of tree or in a collapsed branch it will be highlighted Press the Close Find First Find Next or Find A11 buttons to close the dialog or find the first or next occurrence of the query respectively Alternatively use the From File button to find all nodes that match any line of a given input file The Match Whole Respect Case and Regular Expression buttons apply to this type of search too Regular Expressions are powerful and flexible text processing tools They allow to specify complex patterns of text that can be discovered in an input string 12 Example 1 Each of the following represent valid regular expressions and all will successfully match the char acter sequence Escherichia e Escherichia e E e eElscherichia e eElsch aeiou a zJichi Example 2 To select the five taxa simutaneously e g Human Mouse Dog Cat and Rat use the following expression Human Mouse Dog cat Rat and then press Find A11 For an extensive list of mmetacharacters and futher explanations go to http java sun com j2se 1 5 0 docs api java util regex Pattern html 6 3 Message Window
23. m Lactuca Barnadesia Dasyphyllum il E Pi Tree 1 tree Nodes 55 Edges 54 6 of 1065M Figure 3 All labels and tree substructures can be easily edited 5 Daniel H Huson Regula Rupp Vincent Berry Gambette Philippe and Christophe Paul To appear in RECOMB 2009 6 Regula Rupp and Daniel H Huson Summarizing multiple gene trees using cluster networks In WABIO8 2008 20 Index About 9 13 Add Tree or Network 10 angular edges 12 apply a command 16 apply to all trees 16 Batik 18 BMP 16 circle nodes 12 circular 14 citing the program 3 Clear Formatting 11 click selection 14 Close 5 12 Cluster method 8 cluster network 8 Collapse 7 Collapse at Level 7 Collapse Complement 7 Command 16 command 16 Command line Syntax 10 Consensus Bar 11 Contract view horizontally 10 Contract view vertically 10 Convert text to graphics 13 Copy 5 11 curved edges 12 default font setting 12 Delete Taxa 6 Dendroscope About 9 13 Dendroscope_macos_2 7 4 dmg 4 Dendroscope_unix_2 7 4 sh 4 Dendroscope_windows_2 7 4 exe 4 Deselect All 6 Deselect Edges 6 Deselect Nodes 6 Disclaimer 3 Draw Circular Cladogram 4 8 10 Draw Circular Phylogram 4 8 10 Draw Internal Circular Cladogram 4 8 10 Draw Radial Cladogram 4 8 10 Draw Radial Phylogram 4 8 10 Draw Rectangular Cladogram 4 8 10 Draw Rectangular Phylogram 4 8 10 Draw Slanted Cladogram
24. nonia Coreopsis Coreopsis Tagetes Scaevola rphatheca Blennosperma Blennosperma Chromolaena Campanula Chromolaena Campanula Tagetes Scaevola Tagetes Scaevola Felicia Stokesia Felicia Stokesia Echir Dimorphotheca Echinops Dimorphotheca Gazania Senecio Nk E J 1 R e l Tree 1 Treel Nodes 55 Edges 54 A 1801 4 Tree 1 Tree Nodes 55 Edges S4 180f 4144 Tree 1 Treel Nodes 55 Edges S4 Tree 1 Treel Nodes SS Edges 54 1Bot4 Figure 1 Illustration of the eight views possible with Dendroscope Upper line Rectangular Phylogram Rectangular Cladogram Slanted Cladogram Circular Phylogram Lower line Circular Cladogram Internal Circular Cladogram Radial Phylogram Radial Cladogram 11 Acknowledgements This program includes software developed by the Apache Software Foundation http www apache org namely the Batik library for generating image files It also uses MR JAdapter a Java package used to help construct user interfaces for the Apple Macintosh This program uses Daniel Huson s unpublished jloda library which is also used by SplitsTree4 http www splitstree org 2 18 ncbi taxonomy tree Dendroscope BETA version 0 21 built 16 Feb 2007 File Edit Select Option View Window Baad i f ore FSM QEECKGKG D Symphalangus _syndactylus_syndactylus i LeSymphalangus_syndactylus 1 Bunopithecus_hoolock Gorilla_gorilla_beringei
25. of the modified and or formatted tree By convention we use the suffix dendro for Dendroscope files 14 8 1 Dendroscope Files Dendroscope saves trees in a simple text based format with the file extension dendro It contains the tree in Newick notation and additional machine readable information on the view selections coloring etc of the saved trees Trees can also be saved in Nexus and Newick format However when these formats are used all information on the layout of the trees fonts colors linewidths etc are lost 8 2 Nexus files Dendroscope can read a Nexus file that contains a Nexus trees block and can export trees in this format 8 3 Newick files Dendroscope can read Newick files and can export trees in this format 8 4 Extended Newick format and rooted phylogenetic networks The Extended Newick format was designed as an extension of the Newick format to be able to describe rooted phylogenetic networks in bracket notation Unfortunately there is not just one such format but a number of different ones Dendroscope implements a version of the Extended Newick format that arose out of discussions that took place during the Phylogenetics Programme at the Isaac Newton Institute in 2007 In Dendroscope a rooted phylogenetic network is described as a single line of extended Newick format using brackets as in the description of a rooted phylogenetic tree in the standard Newick format with additional labels placed at the
26. ortions of the tree Selecting the View gt Use Magnifier item adds a magnifier layer to the view e Magnifier band For all rooted views rectangular and slanted view a magnifier band is laid over the tree e Magnifier disk For all unrooted views radial and circular tree view a circular magnifier is laid over the tree The magnifier can be pulled to a desired position by grabbing its frame with the mouse The radius width of the magnifier can be changed by dragging the rhomb at the magnifier s border line The zoom factor of the magnifier can be changed via the button Two magnifier modes are available depending on the current tree view 7 3 Navigating trees with keys and mouse wheel Dendroscope allows one to browse and analyze trees Navigating trees is facilitated by some key bindings e Scrolling Hold down the Shift button and use the mouse wheel to scroll top down Hold down the Alt and Shift buttons and use the mouse wheel to scroll right left e Zooming Use the mouse wheel to zoom the tree Zooming is centered on the current mouse position Alternatively use the arrow keys to scroll the tree or additionally press the shift key to zoom the graph in horizontal or vertical direction Use the alt and control keys for acceleration e Rotating For circular and radial drawings use the shift key and left and right arrow keys to rotate the tree 8 File Formats Dendroscope uses its own file format to store the data
27. oscope OOO _ SunflowersA tre_coy dendro 2 Dendroscope OOO _ SunflowersA tre_cpy2 dendro 3 Dendroscope OOO SunflowersA trecpy3 dendro 4 Dendroscope aBa l 3300 HP EM QEECKGSKS A Samaa i F HH HA MEM Q EESAGORO GOSS E gen HP MEM Q EECAGSKSSOS SE E 700 HP EQ EEXSKGORAD 0 11 0 Piptocarpa Nicotiana Mi Nicotiana E Campanula L Campanula Achillea p Scaevola la Scaevola Canthgmaus morron Bier phorhe Bimba cae on a ot senado gmo ota Senet Alar L imao lt Ciencia Gazania Gazania Gazania Leva L feninops a hinos Echinops Fela Fehca Felicia vada Chromolae mee pi Lp Blennosperma Le ennosperma Blennosperma Coreopsis Dasyphyllum opis Coreopsis Coreopsis m p Vernonia Vernonia Vernonia lennosperma Cacosmia Cacosmia Cacosmia L i Cicherum ichoriur ome A a Cronlen C eri K i Faveria L Lo P p E eanna pe ie hs Fehanths Tragopogon ra ragapogon Chrysanthemum ysanthermum Cheysanthe mum T upton Stor tpn Stokesia samadesia na Barnage Barnadesia jarna madesia basin gt tT Dasvohyiium Dasyphyilum e 000 SunflowersA tre_cpy4 dendro 5 Dendroscope 000 SunflowersA tre_cpy5 dendro 6 Dendroscope 000 SunflowersA tre_cpy6 dendro 7 Dendroscog O O SunflowersA tre_cpy7 dendro 8 Dendroscope Faveria Helianthus Carthamnus Achillea Faveria Helianthus Tras Carthamaus Achillea Cichorium Cichorium Eupatorium Cacosmia Cacosmia Laa Vernonia Ver
28. ossible values left right random none rotatesubtree Rotate all children of all selected nodes swapsubtree Swap subtree below selected node s reset labelpositions Reset all node label positions center Center the tree rotate angle number Rotate the whole tree by the given angle in radian set hflip bool Flip the tree horizontally rotatelabels Rotate the labels of selected nodes Adding creating and modifying trees add tree newick tree Add the specified tree to the list of trees duplicate Duplicate the current window extractsubtree Extract the subtree induced by the currently selected nodes extractlsatree Extract the LSA tree from a rooted network remove taxa selected names Remove all selected taxa if taxa selected otherwise remove named taxa compute consensus value Compute a consensus tree or network of a set of trees possible values Strict Majority Loose Network LSA remove innerlabels Remove all labels of inner nodes apply command Applies the given command to all trees in the file Selection and Deselection select all Select all nodes and edges select nodes Select all nodes 16 select edges select previous select labelednodes select leaves select subtree select subpart select nonterminal select intermediate select root select special select invert deselect all deselect nodes deselect edges list taxa selected Searching Sele Sele Sele Sele
29. rmatting click File gt Save As generating a dendro project file You can alos export the tree s by clicking File gt Export Choose one of the export formats newick nexus dendro Note that only by saving a formatted tree as a dendro project file you can save the formatting with the tree 5 Main Window The Main window is used to display the taxonomy and to control the program via the main menus We now discuss all menus of the Main window 5 1 The 5 2 The File Menu File menu contains the following file related items The File gt New item opens an empty Dendroscope document The File Open item provides an Open File dialog to open one or more Dendroscope files see Section 8 or tre or nexus files containing input data The File gt Recent Files item can be used to re open a recently opened file The File Save item can be used to save the current tree and layout as Dendroscope project file The File Save As item can be used to save the current tree s as Dendroscope project file dendro with the topology and layout The File Export item can be used to export the current tree s to Newick or Nexus file format Note that only the topology but not the layout will be saved The File gt Duplicate item opens an additional window of Dendroscope containing the current tree The File Export Image item opens the Export Image dialog which is used to save the current tree in a number of different
30. rview of its features e There are 8 different tree views available e g phylogram cladogram or radial views e Its novel navigational features facilitate the analysis of large trees e It provides several tree manipulating functions like rerooting subtree rotating tree flipping and formating features like renaming coloring or resizing edges nodes and labels e A comprehensive set of export formats for the generation of images is available e User formated trees can be saved as a Dendroscope project file or as nerus or Newick tree files e Tree structures single or multiple can be loaded from tre Newick format or nexus files or entered manually e Rooted phylogenetic networks can be entered and visualized using the Extended Newick format 1 e The program facilitates the computation of consensus trees and networks from a set of input trees 3 Obtaining and Installing the Program Dendroscope is written in Java and requires a Java runtime environment version 1 5 or later freely available from www java org Dendroscope is installed using an installer program that is freely available from www dendroscope org There are three different installers targeting different operating systems e Dendroscope windows_2 7 4 exe provides an installer for Windows e Dendroscope macos_2 7 4 dmg provides an installer for MacOS e Dendroscope_unix_2 7 4 sh provides a shell installer for Linux and Unix Alternatively Dendroscope will
31. the names of images files and for each match found Dendroscope shows the image near the node representing the given taxon The Options Image Size item is used to set the size of the image for the currently selected nodes The Options Image Position submenu is used to determine the relative positions of images in relative to the corresponding nodes North South East West Radial The Options Strict Consensus item is used to compute the strict consensus of a set of trees The Options gt Loose Consensus item is used to compute the loose consensus Of a set of trees The Options Majority Consensus item is used to compute the majority consensus of a set of trees e The Options gt LSA Consensus item is used to compute the LSA consensus of a set of trees The Options Network Consensus item is used to compute a rooted network consensus of a set of trees If the input set contains more than two trees then the user can set a threshold that determines the percentage of input trees that a cluster must be contained in to make it into the output rooted network The user can also decide whether the program should come a cluster network 6 that shows the clusters in a hardwired representation a galled network 5 that represents the clusters in a topologically restricted softwired representation ora minimum network that attemps to represent the clusters in a network of minimum level as described in Van Iersel et al submitted 200
32. the size of all selected edges ract tree horizontally ract tree vertically Expand tree horizontally Expand tree vertically Zoom to current selection of nodes Zoom to fit whole tree in window Rese t the scaling of the tree Turn magnifier on or off Set Set Set magnifier radius magnifier displacement power the magnifier all mode load imagedir directory name Load image files from named directory Images are placed next to taxa of same name set imageheight num set imagelayout value Special purpose update metasim set dirty bool set vint bool set scalebar bool setprop name boolean Other version help about quit Set Set the height of the images associated with all selected nodes the layout used for images possible values north south east west radial Update the computation Run Set Set Set Set List List List metasim commands the dirty status of a document show version in window title mode show scalebar mode the boolean value of a named property version info this help information about Dendroscope 17 Find an 10 Examples Figures 1 through 3 illustrate the major views possible with Dendroscope as well as the action of the Magnifier and the editing possibilities foo SunflowersA tre dendro Dendr
33. w edgelabels bool show edgeweights bool show nodelabels bool Set the margin around the tree Set minimum threshold for representing subtrees by approximate shapes Show Show Show show intermediatenodelabels bool set maintainedgelengths bool set eshape value set nshape value set radiallabels bool set sparselabels bool set color color set bgcolor color set labelcolor color set edgewidth number set nodesize number Scaling contract direction horizontal contract direction vertical expand direction horizontal expand direction vertical zoom selection zoom fit reset view Controlling the magnifier set magnifier bool set magradius number set magdisplacement number set magnifyallmode bool Adding images to nodes Show When Set Set Set Set Set Set Set Set Set Cont Cont or hide edge lbels or hide edge weights or hide node labels or hide labels of intermediate nodes set edge lengths cannot be changed when not set edges can be stretched the shape of selected edges possible values polygon quadratic cubic the shape of selected nodes possible values rect oval radial layout of node labels sparse layout of node labels in which labels that would overlap others are not shown the color of all selected nodes and edges the background color of all selected nodes the label color of all selected nodes and edges the line width of all selected edges
34. ws are openend they are listed at the end of the window menu 5 8 Toolbar For easier access of frequently used functions a Toolbar is provided with the following functions e File gt 0Open File gt Save As File gt Print File gt Export Image Edit Format e The Expand view vertically button expands the tree vertically e The Contract view vertically button shrinks the tree vertically e The Expand view horizontally button expands the tree horizontally e The Contract view horizontally button shrinks the tree horizontally e The Rotate Left button rotates the whole tree to the left e The Rotate Right button rotates the whole tree to the right e View gt Zoom to Fit View gt Fully Contract View gt Fully Expand View Use Magnifier Tree gt Draw Rectangular Phylogram Tree gt Draw Rectangular Cladogram Tree gt Draw Slanted Cladogram Tree gt Draw Circular Phylogram Tree Draw Circular Cladogram Tree Draw Internal Circular Cladogram Tree gt Draw Radial Phylogram Tree gt Draw Radial Cladogram Edit gt Find Tree gt Ladderize Left Tree gt Ladderize Right Tree Ladderize Random Tree Ladderize Random Edit gt Reroot Edit Swap Subtree 10 5 9 Context Menus A right mouse click on a node opens a context menu which allows to edit the node label open the Format Panel show or hide node labels copy the node label select the subtree starting from this node and swap the
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