User Manual for Dendroscope V1.4
Contents
1. Spermophilus atricapillus Spermophilus washingtoni INI Spermophilus parryii_lyratus 4 Tree 1 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 17 ENEE 2 Dendroscope b ioj xi File Edit Select Option View Window Base i 320 HP HEM A EESAGOHAO A m Nicotiana Campanula Scaevola Stokesia Dimorphotheca Senecio Gerbera Gast pa Format SunflowersA 55 nexus 2 Dendroscope adm xd morus File Edit E O z Boia nat Echinops Felicia Tagetes Chromolaena Blennosperma Coreopsis Vernonia Cacosmia Cichorium Node Size 2 X Achillea 5 Carthamnus Node Shape none b A Flaveria Piptocarpa Edge Width E Labels Rotate Left Rotate Right Tragopogon Lactuca Barnadesia Dasyphyllum Treez1 tree Nodes 55 Edges 54 6 of 1065M IL Figure 3 All labels and tree substructures can be easily edited 18 Index About 8 12 Duplicate 5 9 Allow Reshape i 6 angular edges 10 apply a command 14 apply to all trees 14 edge labels 8 edge weights 8 edge width 10 Edit 5 Batik 15 Edit Copy Image to Clipboard 5 BMP 13 Edit Delete Taxa 5 Edit2. 16 3 ncbi taxonomy tree Dendroscope BETA version 0 21 built 16 Feb 2007 File Edit Select Option View Window BsB4E 330 4 HEM QA EESO amp E Symphalangus_syndactylus 1 Bunopithecus_hoolock Gorilla gorilla beringei Gorilla gorilla gorilla s e Gorilla gorilla graueri Gorilla gorilla uellensis Gorilla gorilla diehli n Pan paniscus an troglodytes schweinfurthii Pan troglodytes troglodytes Pan troglodytes verus Pan troglodytes vellerosus Homo sapiens neanderthalensis Esmanur Pongo sp Lr Pongo_pygmaeus_abelii E Pongo_pygmaeus_pygmaeus Japanese monkeys se marmosets unidentified monkey r Cynocephalus variegatus 339 of 414M Nodes 326289 Edges 326288 File Edit Select Option View Window i amp eB ds e pnBI QEECKSKSM gt Ateles panico Ateles fusciceps Ateles_ Pe 2004 Brachyteles_hypoxanthus Aotus_azarai_boliviensis Callicebus donacophilus donacophilus Pithecia pith ecial Chlorocebus_aethiops_aethiops Cercopithecus_diana 1 Cercopithecus_pogonias_grayi Macaca speciosa Hylobates moloch Gorilla gorilla beringei a gPan_paniscus E Pan_troglodytes_verus Pan troglodytes vellerosus Homo sapiens neanderthalensis Elomo sanien 2i Homo_sapiens 1 Pongo sp Pongo pygmaeus abelii Japanese monkeys Cynocephalus variegatus Ochotona_erythrotis Marmota olympus m
3. uppermost in the view e The Tree Ladderize Right item is used to order the tree so that the largest clades 5 6 appear rightmost lowermost in the view e The Tree Ladderize Random item is used to order the clades randomly View Menu The Views menu contains items for scaling the tree using the magnifier and showing hiding labels e The View Zoom to Fit item is used to scale the tree to fit the window e The View Fully Contract item is used to contract the tree e The View Fully Expand item is used to expand the whole tree 5 7 The The View Use Magnifier item is used to turn the magnifier functionality on and off The View 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 Hide Node Labels item is used to hide all node labels The View Show Edge Weights item is used to make edge weights visible The View Show Edge Labels item is used to make edge labels visible The View Hide Edge Labels item is used to hide edge labels The View 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 posi
4. 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 15 ooo SunflowersA tre dendro Dendroscope OOO _ Sunflowersa tre cpy dendro 2 Dendroscope OOO SunflowersA tre_cpy2 dendro 3 Dendroscope O OO __ SunflowersA tre_cpy3 dendro 4 Dendroscope SBS a ll f om HF HEN QEESACORDA 4 aBSS 8 FF HH HA MAMA EESKOOHS GOSS l 3 en AP MIB QEEIKOSKGISGD amp E Zw AP MAMA EEIAOASD 41 0 10 Nicotiana Nicotiana manda cen d ch u ee E Cichorium L c norphotheca ce Medo rA Cacosmia mL Casan L ceno inops Feli T licia Vernonia ragetes agetes ivomolsens Chromolaena cuida Blennosperma Blennosperma 1 Coreopsis Coreopsis Vernonia Vernonia Blennosperma Cacosmia Cacosmia Cichorium Cien mL Achilles rata arthamnus sr EE Faveria iocarpa roca E recia Helianthus I Chreanthe mam a Eupatorium tapar cuca cuca Barnadesia Barnadesia C pila Dasyphyl OOO SunflowersA tre cpy4 dendro 5 Dendroscope 000 SunflowersA tre cpy5 dendro 6 Dendroscope QOO Sunflowerss tre cpy6 dendro 7 Dendroscof SunflowersA tre cpy7 de
5. eua Window Size 8 Tree 7 Iree Draw Circular Cladogram 4 7 9 Zoom to Fit 7 9 Iree Draw Circular Phylogram 4 7 9 Tree gt Draw Internal Circular Cladogram 4 7 9 Iree Draw Radial Cladogram 4 7 9 Iree Draw Radial Phylogram 4 7 9 Tree Draw Rectangular Cladogram 4 7 9 Tree Draw Rectangular Phylogram 4 7 9 Iree Draw Slanted Cladogram 4 7 9 Tree Ladderize Left 7 9 Tree Ladderize Random 7 9 Tree Ladderize Right 7 9 Tree Next Tree 7 Tree Previous Tree 7 21
6. for selected nodes Visualization set window width num height num x num y num Set size and location of main window set font name Set font by name set autolayoutlabels bool Set auto layout of labels set margin left num right num top num bottom num Set the margin around the tree Show edgelabels bool Show or hide edge lbels show edgeweights bool Show or hide edge weights show nodelabels bool Show or hide node labels show intermediatenodelabels bool Show or hide labels of intermediate nodes set maintainedgelengths bool When set edge lengths cannot be changed when not set edges can be stretched set eshape value Set the shape of selected edges possible values polygon quadratic cubic set nshape value Set the shape of selected nodes possible values rect oval set radiallabels bool Set radial layout of node labels set sparselabels bool Set sparse layout of node labels in which labels that would overlap others are not shown set color color Set the color of all selected nodes and edges set bgcolor color Set the background color of all selected nodes set labelcolor color Set the label color of all selected nodes and edges set edgewidth number Set the line width of all selected edges set nodesize number Set the size of all selected edges Scaling contract direction horizontal Contract tree horizontally contract direction vertical Contract tree vertically expand direction horizontal Expand t
7. 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 select edges Select all edges select previous Select all labeled nodes as in previous window select leaves Select all leaves select subtree Select all nodes in subtrees below selected select subpart Select part of subtree select nonterminal Select all non terminal nodes select intermediate Select all intermediate nodes select root Select root select special Select all special edges select invert Invert the current selection deselect all Deselect all nodes and edges deselect nodes Deselect all nodes deselect edges Deselect all edges list taxa selected List all currently selected taxa Searching find pattern Find and select the next taxon matching the given pattern Java regular expression findall pattern Find and select all taxa matching the given pattern find file Find and select all taxa matching a line in the given file Collapsing and uncollapsing nodes collapse all Collapse all nodes collapse selection Collapse all selected nodes collapse complement Collapse the complement of all selected nodes collapse level number Collapse all nodes at the given level distance from root uncollapse all Uncollapse all nodes 14 uncollapse selection Uncollapse all selected nodes uncollapse subtree Uncollapse whole subtree
8. Find 5 9 10 circle nodes 10 Edit Find Again 5 circular 12 Edit Format 4 6 9 10 citing the program 3 Edit Reorder Subtree 5 Clear Formatting 10 Edit Reroot 5 9 click selection 12 Edit Rotate Subtree 5 Close 5 11 Edit Swap Subtree 5 9 Collapse 6 Enter Command 14 Collapse at Level 7 Enter Tree 8 Collapse Complement 6 EPS 11 13 Command 14 Execute Command 8 command 14 Expand view horizontally 9 Command syntax 8 Expand view vertically 9 Contract view horizontally 9 Export 4 5 Contract view vertically 9 Export Image 4 5 9 11 Convert text to graphics 11 Extract Subtree 7 Copy Image to Clipboard 5 curved edges 10 File 4 File Close 5 default font setting 10 File Duplicate 5 Delete Taxa 5 File Export 4 5 Dendroscope About 8 12 File Export Image 4 5 9 11 Dendroscope macos 1 4 dmg 3 File New 4 Dendroscope unix 1 4 sh 3 File Open 4 9 Dendroscope windows_1 4 exe 3 File Print 4 5 9 Deselect All 6 File Quit 5 Deselect Edges 6 File Recent Files 4 5 Deselect Nodes 6 File Save 5 Disclaimer 2 File Save As 4 5 9 Draw Circular Cladogram 4 7 9 Find 5 9 10 Draw Circular Phylogram 4 7 9 Find Again 5 Draw Internal Circular Cladogram 4 7 9 Find All 11 Draw Radial Cladogram 4 7 9 Find First 11 Draw Radial Phylogram 4 7 9 Find Next 11 Draw Rectangular Cladogram 4 7 9 finding taxa from a file 11 Draw Rectangular Phylogram 4 7 9 font fami
9. R d 8 3 Newick files gt sssr cueg 8 4 Graphics Formats s sa sasare agesas 9 Commands 10 Examples 11 Acknowledgements References Index 1 Introduction Disclaimer This software is provided AS IS without 12 TI 12 tLe X4 A 4echge o Bom ORAS 12 Right deed E Ab tegens t doe tut d 12 13 LORS d om x oA ER XN de Rue s 13 LAE Sues Gob eye Ete t Roe Gye eg 13 one dE uy ea E E Eds 13 A gon Ae SEX ud At a 13 14 15 15 16 19 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 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 2 2 Program Overview Dendroscope is a platform independent software written in Java that enables conveniently to browse phylogenetic trees with up to hundreds of thous
10. User Manual for Dendroscope V1 4 Daniel H Huson Daniel C Richter Christian Rausch and Regula Rupp July 4 2008 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 mi BUIN ss haee A ee ROUES ds no XCx e we E b e RAYS e Ale n GE IE Meme e ei 4E suum RIO Rex QUE 9 wed Wow POE OR EURO Xue AE ww Da Geleet Men e ok ood nghe xo ae De Eod dd Eom e ROT a OA Options Menu uuo m9 3 SRR EE cw X4 Ee he ee A A au Yes DIGNUS seb ine Ru A REGEM He Kok Denm Rum SUD ee ee ee 50 Yew Men 2 eoa oe Re RR a OR s vob Ro eoe B EUR OR o e 5 7 Window Mem i sco scosese o o n Ls Tob 2229 gsx A 5 9 Context Menus e 5 10 Sidebar 22 e je m m d n ok 86225542 DIL GADA a 2x ce ee Ae eg dew REOR 6 Additional Windows 61 Format Pawel sos ko kx Rs Oe Find Window ioa scene cR eR EO 9 6 3 Message Window 6 4 Export Image Dialogg Go About Window oe oec a RO ui E Res 7 Additional Features 7 1 Using the Mouse to Select 7 2 Magnifier Functionality 7 3 Navigating trees with keys and mouse wheel 8 File Formats 8 1 Dendroscope Files B Nerus BS uu soos RR Roo ho oe R
11. ands of taxa Here is an overview 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 It provides several tree manipulating functions like rerooting subtree rotating tree flipping and formating features like renaming coloring or resizing edges nodes and labels A comprehensive set of export formats for the generation of images is available 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 3 Obtaining and Installing the Program Dendroscope is written in Java and requires a Java runtime environment version 1 4 or newer 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 1 4 exe provides an installer for Windows e Dendroscope macos 1 4 dmg provides an installer for MacOS e Dendroscope unix 1 4 sh provides a shell installer for Linux and Unix Alternatively Dendroscope will 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 produc
12. can also be selected by clicking on them shift clicking to extend a selection or by shift clicking and then dragging the mouse to perform rubber band selection in which all objects contained within a dragged rectangle are selected Note Unlike many programs where rubber band selection is performed by click dragging Dendro scope requires that you shift click and drag 7 2 Magnifier Functionality Dendroscope provides the user with a magnifier functionality that can be used to magnify portions of the tree Selecting the View 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 4 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 ri
13. d 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 Find item Its purpose is to find taxa 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 If the Match Whole item is selected then only taxa or labels matching the complete query string will be returned e Ifthe Respect Case item is selected then the case of letters is distinguished in comparisons 10 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 Example Each of the follow
14. ew 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 Zoom to Fit View Fully Contract View Fully Expand View Use Magnifier Tree Draw Rectangular Phylogram Tree Draw Rectangular Cladogram Tree Draw Slanted Cladogram Tree Draw Circular Phylogram Tree Draw Circular Cladogram Tree Draw Internal Circular Cladogram Tree Draw Radial Phylogram Tree Draw Radial Cladogram Edit Find Tree Ladderize Left Tree Ladderize Right Tree Ladderize Random Tree Ladderize Random Edit Reroot Edit Swap Subtree 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 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 Sidebar The Sidebar 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 tree
15. ext 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 possible 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
16. ght left e Zooming Use the mouse wheel to zoom the tree Zooming is centered on the current mouse position Alternatively use the f and arrow keys to zoom Additionally press the the Shift key for acceleration 12 e Hotating Hold down the Alt button and use the mouse wheel to rotate the tree Alterna tively use the and the arrow keys to rotate Additionally press the the Shift key for acceleration 8 File Formats Dendroscope uses its own file format to store the data of the modified and or formatted tree By convention we use the suffix dendro for Dendroscope files 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 Graphics Formats The following graphics formats are supported how to open the Export Image dialog see 6 4 e JPEG Joint Photographic Experts Group e GIF Graphics Interchange Format e EPS E
17. ing represent valid regular expressions and all will successfully match the char acter sequence Escherichia e Escherichia e E e eEjscherichia e eEjsch aeiou a z ichi For an extensive list of metacharacters and futher explanations go to http java sun com j2se 1 5 0 docs api java util regex Pattern html 6 3 Message Window The Message window is opened using the Window 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 Export Image item This dialog is used to save an image of the current tree in a number of different formats see Section 8 4 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 11 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 7 Additional Features 7 1 Using the Mouse to Select Nodes edges and labels
18. its the program Under MacOS this item is contained in the Dendroscope menu Edit Menu Edit menu contains the usual edit related items The Edit Copy Image to Clipboard item is used to copy the current tree as an image which can be directly pasted into any picture editing software The Edit Find item opens the Find window which can be used to search for taxa and labels The Edit 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 The Edit Swap Subtree item swaps the subtree at the specified node see also Section Tad The Edit Rotate Subtree item rotates the subtree at the specified node The Edit Reorder Subtree 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 5 3 The 5 4 The The Allow Reshape i tem is used to set the allow reshape mode in which the user is allowed to move individual nodes and internal edge points The Edit 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
19. lect Non Terminal 6 Select Root 6 Select Subtree 6 Select Deselect All 6 Select Deselect Edges 6 20 Select Deselect Nodes 6 Type setting conventions 3 Select Invert Selection 6 Select List Selected Taxa 6 Uncollapse 6 Select Scroll to Selection 6 Unix 3 Select Select All 6 Use Magnifier 4 8 9 12 Select Select Edges 6 Select Select Leaves 6 Select Select Nodes 6 Select Select Non Terminal 6 Select Select Root 6 Select Select Subtree 6 Set Window Size 8 shift click and drag selection 12 shift click selection 12 Show Edge Labels 8 Show Edge Weights 8 Show Node Labels 8 show hide labels 10 View Fully Contract 7 9 View Fully Expand 7 9 View Hide Edge Labels 8 View Hide Node Labels 8 View Magnify All Mode 8 View Radial Labels 8 View Reposition Labels 8 View Show Edge Labels 8 View Show Edge Weights 8 View Show Node Labels 8 View Sparse Labels 8 View Use Magnifier 4 8 9 12 View Zoom to Fit 7 9 Sidebar 9 Views 7 Sidebar Clear Formatting 10 i Sidebar Duplicate 9 Webstart application 4 Sidebar Remove 10 Window 8 Sidebar Rename 9 Window About 8 12 Sparse Labels 8 Window Command syntax 8 square nodes 10 Window Enter Command 14 Statusbar 10 Window Enter Tree 8 straight edges 10 Window Execute Command 8 SVG 13 Window How to Cite 8 Swap Subtree 5 9 Window Message Window 8 11 Toolbar 9
20. ly 10 Draw Slanted Cladogram 4 7 9 font size 10 19 font style 10 Format 4 6 9 10 Format Panel 10 From File 11 Fully Contract 7 9 Fully Expand 7 9 GIF 13 graphics formats 13 Hide Edge Labels 8 Hide Node Labels 8 How to Cite 8 How to cite 3 1 6 Invert Selection 6 JPEG 13 key bindings 12 Ladderize Left 7 9 Ladderize Random 7 9 Ladderize Right 7 9 Linux 3 List Selected Taxa 6 MacOS 3 5 magnifier band 12 magnifier functionality 12 Magnify All Mode 8 Main 4 Match Whole 10 Message 11 Message Window 8 11 MRJAdapter 15 Navigating trees 12 New 4 Next Tree 7 Nexus trees block 13 node color 10 node shapes 10 node size 10 Open 4 9 Open File 4 Option Collapse 6 Option Collapse at Level 7 Option Collapse Complement 6 Option Extract Subtree 7 Option Uncollapse 6 Options 6 Options Save Font As Default 10 outgroup 5 PDF 13 PNG 13 Previous Tree 7 Print 4 5 9 Quit 5 Radial Labels 8 Recent Files 4 5 Regular Expression 11 Remove 10 Rename 9 Reorder Subtree 5 Reposition Labels 8 Reroot 5 9 Respect Case 10 rotate labels 10 Rotate Left 9 Rotate Right 9 Rotate Subtree 5 rubber band selection 12 Save 5 Save As 4 5 9 Save Font As Default 10 Save visible region 11 Save whole image 11 Scroll to Selection 6 Select 6 Select All 6 Select Edges 6 Select Leaves 6 Select Nodes 6 Se
21. matted 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 File Menu The File menu contains the following file related items e The File New item opens an empty Dendroscope document e 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 5 2 The The File Recent Files item can be used to re open a recently opened file The File gt 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 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 graphics formats see Section 8 4 The File Print item is used to print the current tree The File Close item closes the current window In case only one window is opened the application exits The File Quit item qu
22. ncapsulated PostScript SVG Scalable Vector Graphics e PNG Portable Network Graphics e BMP Bitmap e PDF Portable Document Format 13 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 cancel 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 pening and saving files open file name init command Open the named file in the current window if empty otherwise in a new window 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 n
23. ndro 8 Dendroscope suit 330 HE SAT Q EESKOOAD A Ja i ZH HP MBN QEECKOSKS A LAA i gon HP MAMA EESKODA i E FZ ee HP BN QESEKOSKS M Carthamnus Tragopogon Achillea Chrysanthemum Chrysanthemum Cichorium Eupatorium Cichorium Eupatorium Cacosmia uawa Cacosmia latua Vernonia Vernonia Coreopsis Coreopsis Tagetes Scaevola theca Blennosperma Blennosperma Chromolaena Campanula Chromolaena Campanula Tagetes Scaevola Tagetes Scaevola Felicia Stokesia Felicia Stokesia chi Dimorphotheca Echinops Dimorphotheca Gazania zie tL J M Nodes 55 E ges 54 180 414 Tree 1 Tree Nodes 55 Edges 54 B Nodes 55 E ges 54 TT Figure 1 lllustration 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 http www splitstree org l References 1 D H Huson and D Bryant Application of phylogenetic networks in evolutionary studies Molec ular Biology and Evolution 23 254 267 2006 Software available from www splitstree org 2 D H Huson D C Richter C Rausch T Dezulian M Franz and R Rupp Dendroscope An interactive viewer for large phylogenetic trees BMC Bioinformatics 8 460doi 10 1186 1471 2105 8 460 2007 Software available from www dendroscope org
24. ree horizontally expand direction vertical Expand tree vertically zoom selection Zoom to current selection of nodes zoom fit Zoom to fit whole tree in window reset view Reset the scaling of the tree Controlling the magnifier set magnifier bool Turn magnifier on or off set magradius number Set magnifier radius set magdisplacement number Set magnifier displacement power set magnifyallmode bool Set the magnifier all mode Adding images to nodes load imagedir directory name Load image files from named directory Images are placed next to taxa of same name set imageheight num Set the height of the images associated with all selected nodes set imagelayout value Set the layout used for images possible values north south east west radial Special purpose update Update the computation metasim Run metasim commands set dirty bool Set the dirty status of a document set vint bool Set show version in window title mode set scalebar bool Set show scalebar mode setprop name boolean Set the boolean value of a named property Other version List version info help List this help about List information about Dendroscope quit Quit the program 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 11 Acknowledgements This program includes software developed by the Apache Software Foundation http
25. s 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 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 e The Remove item can be used to remove a tree for the list of trees 5 11 Statusbar The Statusbar at 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 6 Additional Windows 6 1 Format Panel The Format Panel can be opened via Edit 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 e Edges can be assigned three types of shapes straight edges curved edges and angular edges the effect of which depends on the current view e 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 e If a selected node or edge has a label then you can choose its font family font style or font size e Labels can be switched on and off an
26. 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 Select Nodes item is used to select all nodes The Select Select Edges item is used to select all edges The Select Deselect All item is used to deselect all nodes edges and labels that are currently selected The Select Deselect Nodes item is used to deselect all nodes that are currently selected The Select Deselect Edges item is used to deselect all edges that are currently selected The Select Select Leaves item is used to select all leaves with their labels The Select Select Subtree item is used to select a subtree of a selected inner node The Select Select Root item is used to select the root node of the tree The Select Select Non Terminal item is used to select all non terminal nodes and edges The Select Invert Selection item is used to invert the current selection The Select Scroll to Selection item is used to scroll to the current selection The Select List Selected Taxa item is used to list all selected taxa Options Menu Options menu contains items for collapsing nodes and extracting subtrees The Option Collapse item enables to collapse a subtree at a selected specified node The former subtree is replaced by a new edge with label The Option Uncollapse item is used to uncollapse e
27. tion Window Menu Window menu contains a number of window related commands as well as a list of all currently open windows The Window About item opens a splash screen showing the program version In MacOS this can be found under Dendroscope gt About 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 The Window Set Window Size item is used to set the size of the Main window The Window Command syntax item lists all commands supported by the program The Window Execute Command item opens a window that can be used to enter a command see command The Window Enter Tree item opens a window to enter a tree manually in Newick Format If several program windows are openend they are listed at the end of the window menu The Window Message Window item is used to open the Message window 5 8 Toolbar For easier access of frequently used functions a Toolbar is provided with the following functions e File Open File Save As File Print File 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 vi
28. ts 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 Open 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 Draw Circular Cladogram Tree Draw Internal Circular Cladogram Tree 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 Print In case you need a quality image of the tree simply export it to several file formats via File Export Image Finally if you want to save the tree s and the formatting click File Save As generating a dendro project file You can alos export the tree s by clicking File Export Choose one of the export formats newick nexus dendro Note that only by saving a for
29. xpand a selected collapsed subtree The Option Collapse Complement item is used to collapse all subtrees except the currently selected part of the tree e The Option Collapse at Level item is used to collapse all subtrees at the specified level from the root e The Option Extract Subtree item is used to extract a selected subtree to a new file 5 5 The Tree Menu Tree menu contains items for different tree views e The Tree Draw Rectangular Phylogram item is used to draw the tree as rectangular phylogram e The Tree Draw Rectangular Cladogram item is used to draw the tree as rectangular cladogram e The Tree Draw Slanted Cladogram item is used to draw the tree as slanted cladogram e The Tree Draw Circular Phylogram item is used to draw the tree as circular phylogram e The Tree Draw Circular Cladogram item is used to draw the tree as circular cladogram e The Tree Draw Internal Circular Cladogram item is used to draw the tree as circular cladogram with leaves on the inside e The Tree Draw Radial Phylogram item is used to draw the tree as radial phylogram e The Tree Draw Radial Cladogram item is used to draw the tree as radial cladogram e The Tree Previous Tree item is used to switch to the last opened tree e The Tree Next Tree item is used to switch to the next opened tree e The Tree Ladderize Left item is used to order the tree so that the largest clades appear leftmost
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