User Manual for Dendroscope V3.3.2
Contents
1. chicken ie a ra Showing 1 Nodes 43 selected 1 Edges 42 78 of 372M Figure 3 All labels and tree substructures can be easily edited 6 Grass Phylogeny Working Group Phylogeny and subfamilial classification of the grasses Poaceae Annals of the Missouri Botanical Garden 88 3 373 457 2001 7 Katharina T Huber Bengt Oxelman Martin Lott and Vincent Moulton Reconstructing the evolutionary history of polyploids from multilabeled trees Molecular Biology and Evolution 23 9 1784 1791 2006 8 D H Huson SplitsTree analyzing and visualizing evolutionary data Bioinformatics 14 10 68 73 1998 9 D H Huson Drawing rooted phylogenetic networks IEEE ACM Transactions on Computa tional Biology and Bioinformatics 6 1 103 109 2009 10 D H Huson and D Bryant Application of phylogenetic networks in evolutionary studies Molecular Biology and Evolution 23 254 267 2006 25 phyB_rbcL nexml 2 Dendroscope version 3 0 8alpha built 4 Apr 2011 phy8_rbcl hybrid nexml 3 Dendroscope version 3 0 8alpha built 4 Apr 2011 gt Sr OS AENA foe QP i aM Q ESA 444 I 21 lt gt SEBA 48 HOJE 3 0 46 5 HEM A ESAS Bl 14 T ao Showing2. SO Graphics Formal 4 4 4 2 6 be eo ep eee be a b ee Bee eee ek es 9 Using More Memory 10 Commands 11 Command Line Options 12 Examples 12 1 Basic tree view 12 2 Additional tree view features 4 sa u 6 04440 sens a ew a a 12 3 Editing trees 14 14 14 15 15 16 16 16 16 16 17 17 17 17 17 17 18 18 19 21 12 4 Constructing rooted phylogenetic networks 000002 ee 22 a Iamplepti a Gee Be Ba ee oe ye Gee Bo aie he ek ee ek da 23 13 Acknowledgements 23 References 23 Index 28 1 Introduction License Copyright c 2015 Daniel H Huson with some code written by other authors as mentioned in the corresponding source files This program is free software you can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Software Foundation either version 3 of the License or at your option any later version This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details You should have received a copy of the GNU General Public License along with this program If not see http www gnu org licenses 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 result
3. The Advanced Algorithms Simplistic item computes a phylogenetic networks using the sim plistic algorithm 21 Layout Menu Layout menu contains items for different tree and network views 9 The Layout Draw Rectangular Phylogram item is used to draw trees or networks as rectangular phylograms The Layout gt Draw Rectangular Cladogram item is used to draw trees or networks as rectangular cladograms The Layout Draw Slanted Cladogram item is used to draw trees or networks as slanted cladograms The Layout Draw Circular Phylogram item is used to drawtrees or networks as circular phylograms The Layout gt Draw Circular Cladogram item is used to draw as circular cladograms The Layout Draw Inner Circular Cladogram item is used to draw trees or networks as circular cladograms with leaves on the inside The Layout Draw Radial Phylogram item is used to draw trees or networks as radial phylograms The Layout Draw Radial Cladogram item is used to draw trees or networks as radial cladograms The Layout gt Ladderize Left item is used to order trees or networks so that the largest clades appear leftmost uppermost in the view The Layout Ladderize Right item is used to order trees or networks so that the largest clades appear rightmost lowermost in the view The Layout gt Ladderize Random item is used to order the clades randomly The Layout Network Layout item is used to choose the way the network em
4. set labelcolor 225 180 0 to color the taxon AE007869 in the first tree deselect nodes exportimage format PDF file testExport pdf quit 11 Command Line Options Dendroscope has the following Mode g commandLineMode Commands x execute string c commandFile string Configuration E quitOnException command line options Run MEGAN in command line mode Default value false Command to execute at startup do not use for multiple command File of commands to execute in command line mode Quit if exception thrown in command line mode Default value 21 p propertiesFile string Alternate properties file Default value Users huson Librar w hideMessageWindow Hide message window Default value false V version Show version string Default value false S silentMode Silent mode Default value false d debug Debug mode Default value false s hideSplash Hide startup splash screen Default value true Other v verbose Be verbose Default value false h help Show program usage Default value false Launching the program with option g will make the program run ina command line mode first excuting any command given with the x option and then reading commands from the file specified using the c command If no such file is given additional commands are read from standard input Please note that windows will still open when in command line m
5. 15 Replace All 15 Reposition Labels 12 Reroot 6 Reroot By Hybridization Number 10 rooted network consensus 9 rotate labels 14 Rotate Subtrees 6 rSPR Distance Binary Trees 10 rubber band selection 16 Save 6 Save As 5 6 Save Font As Default 14 Save visible region 15 Save whole image 15 Scroll to Selection 8 Select 7 Select All 7 Select Edges 7 Select Induced Network 8 Select Labeled Nodes 7 Select Leaves 7 Select LSA Induced Network 8 Select Nodes 7 Select Non Terminal 7 Select Root 7 Select Spanned Edges 8 Select Special 8 Select Subnetwork 8 Select Advanced Selection 7 Select gt All Panels 7 Select Deselect All 7 Select Deselect Edges 7 Select Deselect Nodes 7 Select From Previous Window 7 31 Select gt Invert Panels 7 Select gt Invert Selection 8 Select gt List Selected Taxa 8 Select gt No Panels 7 Select gt Scroll to Selection 8 Select gt Select All 7 Select Select Edges 7 Select Select Labeled Nodes 7 Select Select Leaves 7 Select gt Select Nodes 7 Select gt Select Non Terminal 7 Select Select Root 7 Select Select Special 8 Selection 14 selection 16 Set Grid 12 Set Image Size 8 Set Tree Name 9 Set Window Size 13 shift click selection 16 Show Borders 12 Show Edge Labels 12 Show Node Labels 12 Show Scale Bar 12 Show Scroll Bars 12 show hide labels 14 Simplistic 11 sim
6. 3 4of4 Nodes 82 Edges 80 556 of 745M Showing D 4of4 Nodes 196 Edges 208 a b Figure 4 a Two phylogenetic trees from the Poaceae dataset from the Grass Phylogeny Working Group 6 The trees have been built from the loci phytochrome B left and ribulose 1 5 biphosphate carboxylase oxygenase large subunit right 18 b The 4 hybrid networks for the trees in a reconstructed by the method presented in 1 11 D H Huson and R Rupp Summarizing multiple gene trees using cluster networks In K Crandall and J Lagergren editors Algorithms in Bioinformatics WABI 2008 volume 5251 pages 296 305 Springer Berlin Heidelberg 2008 12 D H Huson R Rupp V Berry P Gambette and C Paul Computing galled networks from real data Bioinformatics 25 12 2009 13 D H Huson R Rupp and C Scornavacca Phylogenetic Networks Cambridge University Press 2010 14 D H Huson T Dezulian T Kloepper and M A Steel Phylogenetic super networks from par tial trees IEEE ACM Transactions in Computational Biology and Bioinformatics 1 4 151 158 2004 15 D H Huson and S Linz Computing minimum hybridization networks from real phylogenetic trees 2012 Under review 16 Bernard M E Moret Luay Nakhleh Tandy Warnow C Randal Linder Anna Tholse Anneke Padolina Jerry Sun and Ruth Timme Phylogenetic networks Modeling reconstructibil ity and accuracy IEEE ACM Transactions on Computational Biology and B
7. Fit item is used to scale the tree or network to fit the window View gt Fully Contract item is used to contract the tree or network View gt Fully Expand item is used to expand the whole tree or network View gt Use Magnifier item is used to turn the magnifier functionality on and off View gt Magnify All Mode item modifiers the magnification process so that the whole tree gets mapped into the magnifier e The e The e The e The View gt Show Node Labels item is used to make all node labels visible or invisible View gt Show Edge Labels item is used to make edge labels visible or invisible View gt Label Edges By Weights item uses the edge weights as edge labels View Sparse Labels item instructs the program to show only a subset of the taxon labels thus avoiding overlapping labels e The View Radial Labels item instructs the program to rotate leaf labels to match the orientation of the edges that lead to them e The View Reposition Labels item sets all the labels to their original position 12 5 8 Window Menu The Window menu contains a number of window related commands as well as a list of all currently open windows e 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 1 Daniel H Huson Daniel C Richter Christian Rausch Tobias Dezuli
8. cluster network threshold lt value gt galled network threshold lt value gt Distortion1 LSAtree Compute a consensus tree or network of a set of trees compute tanglegram method nnet Compute a tanglegram for two trees or networks using the NeighborNet based heuristic compute triplets2network method simplistic Compute a network using the simplistic algorithm compute hybridization network method Autumn Compute minimum hybridization networks for two rooted phylogenetic trees using the Autumn algorithm Huson in preparatio compute hybridization network method ASCH2011 showdialog false true number0fThreads number Compute minimum hybridization networks for two bifurcating trees on the same taxon set using the Albrecht Scornavacca Cenci and Huson 2011 algorithm compute hybridization number method Autumn Compute the hybridization number for rooted phylogenetic trees using the Autumn algorithm Huson and Linz submitted rerootby method min hybridization number Reroot to trees so as to minimize their hybridization number using the Autumn algorithm Huson and Linz submitted compute hybridization number method ASCH2011 showdialog false true number0fThreads number Compute the hybridization number for two rooted binary trees on the same taxon set compute rspr distance method ASCH2011 showdialog false true number0fThreads number Compute the rSPR distance for two rooted binary trees on the same taxon set compute dist
9. the same label all these nodes are considered to determine the tightest rooting The Edit gt Swap Subtrees item swaps the order of subtrees or subnetworks below the specified node or nodes The Edit gt Rotate Subtrees item rotates the order of the subtrees or subnetworks below the specified node s e The Edit Reorder Subtrees item opens the Reorder subtrees dialog that allows one to specific any type of reordering of the children of the specified node using drag and drop e The Edit gt Delete Taxa item removes the selected taxa in the selected trees or networks e The Edit Unlock Edge Lengths item is used to unlock edge lengths so that the user is allowed to reshape trees or networks by dragging nodes or internal edge points e 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 5 3 Select Menu The Select menu contains items for selecting panels and different sets of substructures of trees or networks e The Select Advanced Selection submenu contains a number of advanced selection menu items that are probably not of general interest e The Select gt A11 Panels item selects all panels e The Select gt No Panels item deselects all panels e The Select Invert Panels item inverts the selection of all panels e The Select gt Select All item is used to select all nodes and edg
10. to specify complex patterns of text that can be discovered in an input string 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 simultaneously 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 further 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 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 6 The dialog permits to specify the file name and where to save the graphics file 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 15 6 5 About Window The About Window is opened using the Window About submenu Dendroscope About in MacOS It reports the version of the
11. 11 Less Panels 12 level 10 level k based 10 License 3 Linux 4 List Selected Taxa 8 Load Taxon Images 8 Loose Consensus 9 loose consensus 9 LSA Consensus 9 LSA consensus 9 MacOS 4 magnifier band 16 magnifier functionality 16 Magnify All Mode 12 Main 5 Majority Consensus 9 majority consensus 9 Message 15 Message Window 13 15 minimum network 10 More Panels 12 MRJAdapter 23 Navigating trees 16 Nested Labels Distance 11 Network Consensus 9 Network for Multi Labeled Tree 10 Network Layout 11 New 5 Next Tree 9 Nexus trees block 17 No Optimization 11 No Panels 7 node color 14 node shapes 14 node size 14 Open 5 Open File 5 Open Recent 5 Options 8 Options Advanced Options 8 Options Collapse 8 Options Collapse at Level 8 Options Collapse Complement 8 Options gt Go to Tree 9 Options gt Image Position 9 Options Load Taxon Images 8 Options gt Next Tree 9 Options gt Previous Tree 9 Options gt Save Font As Default 14 Options gt Set Image Size 8 Options gt Set Tree Name 9 Options Uncollapse 8 Options Uncollapse Subtree 8 outgroup 6 Page Setup 6 Paste 6 Path Multiplicity Distance 11 PDF 18 PNG 18 Previous Tree 9 30 Primodial Consensus 9 primodial consensus 9 Print 5 6 Quit 6 Radial Labels 12 Regular Expression 14 Reorder Subtrees 7 Reorder subtrees 7 Replace 6
12. 5 Tanglegram Figure 5 shows a tanglegram between the first two networks in Figure 4 b 13 Acknowledgements This program includes software developed by the Apache Software Foundation http www apache org namely the Batik J Adapter library for generating image files a Java package used to help construct user interfaces for the Apple Macintosh It also uses MR This program uses Daniel Huson s unpublished jloda library which is also used by SplitsTree4 http www splitstree org 8 10 References 1 B Albrecht C Scornavacca A Cenci and D H Huson hybridization networks Bioinformatics 28 2 191 197 2012 23 Fast computation of minimum _ncbi taxonomy tree Dendroscope version 3 0 8alpha built 4 Apr 2011 lt gt 6082 Lit 200 900 HEM Q EESADORO 444 2H Symphalangus_syndactylus_syndactylus L symphalangus_syndactylus f Bunopithecus _hoolock Goria_gorila_beringei Gorita_gorila_gorita Gorila_gorila_graueri Gorita_gorila_uelensis Gorita_gorita_diohi Pan_paniscus Pan_troglodytes_schweinturthi Pan_troglodytes_troglodytes Pan_troglodytes_verus Pan_troglodytes_vellerosus Homo_sapions_neanderthalensis lomo sapiens Pongo_sp Pongo_pygmaeus_abeli Pongo_pygmaeus_pygmaeus Japanese_monkeys marmosets unidentified_monkey r Cynocephalus_variegatus Cyno
13. 6 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 SVG Scalable Vector Graphics e PNG Portable Network Graphics e BMP Bitmap e PDF Portable Document Format 9 Using More Memory The Dendroscope installer allows you to specify the amount of Dendroscope that the program can use To run Dendroscope with more than 400 MB under MacOS X on an intel Mac edit the file installation dir Dendroscope Dendroscope app Contents Info plist as follows Find the lines lt key gt VMOptions lt key gt lt string gt server Xmx400M lt string gt lt I4J_INSERT_VMOPTIONS gt and replace them by lt key gt VMOptions lt key gt lt string gt server Xmx1000M lt string gt lt I4J_INSERT_VMOPTIONS gt to run using 1 gigabyte for example To run Dendroscope with more more than 400 Mb on a 64 bit unix linux system open the file installation dir Dendroscope in a text editor Find the current memory specification e g Xmx400M and replace it by d64 Xmx100M to run with 1 gigabyte of memory say Note that the flag d64 is necessary to specify 64 bit Java 18 10 Commands The program provides a command interpreter to access all its functionalities A command can be entered either using the Window gt Command Input item or by starting the
14. 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 nexml 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 Open Recent 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 Layout Draw Rectangular Phylogram Layout gt Draw Rectangular Cladogram Layout gt Draw Slanted Cladogram Layout gt Draw Circular Phylogram Layout gt Draw Circular Cladogram Layout Draw Inner Circular Cladogram Layout gt Draw Radial Phylogram Layout 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 Export Image Finally if you want to save the tree s and the formatting click File gt Save As generating a nexml project file You can also export the tree s by clicking File gt Export Choose one of the export formats newick or nexus Note that only
15. Toolbars The Find toolbar can be opened or closed using the Edit gt Find menu item Its purpose is to search labels in the displayed trees or networks Enter a query specifying the text to find in the top text region Use the following check boxes to configure the search e Ifthe Case sensitive item is selected then the case of letters is distinguished in com parisons e Ifthe Whole words only item is selected then only taxa or labels matching the complete query string will be returned e If the Regular Expression item is selected the query is interpreted as a Java regular expression see example further down The scope of the search can be Global or Selection If a searched label is hidden inside a bounding box black opaque area of tree or network or in a collapsed branch it will be selected 14 Press the Close Find First Find Next or Find All buttons to close the toolbar or find the first or next occurrence of the query respectively Press Unselect A11 to unselect the highlighted occurrences The Replace toolbar can be opened or closed using the Edit gt Replace menu item Its purpose is to replace text in the displayed trees or networks Enter a replacement text in the bottom text region Press the Replace or Replace A11 buttons to replace the next or all occurrences of the query with the text in the bottom text region respectively Regular Expressions are powerful and flexible text processing tools They allow
16. User Manual for Dendroscope V3 3 2 Daniel H Huson and Celine Scornavacca July 21 2015 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 ACOE 5 5 4c ka op ee a eB See Ree eke BPE Ee Oe bee OS Ge DO eoi ee e a oe Bh ee Pe ee ee oe ee ee ee E anG 0 3 elect MENG 66 choy bee kee AA a eee Dae Ee a 54 Options Men so ego ea be a he kee eee ee he hee ee eS Gi Algorta Ms io fe ee Pw ee a ae ey ee ee 5 6 Layout Ment 2 6566 ce bee Re ESE eS a eee 5 7 View Menu 5 8 Window Menu 5 9 Toolbar e cocos 5 10 Context Menus 5 11 Status Line Additional Windows 6 1 Format Panel 6 2 Find and Replace Toolbars 6 3 Message Window 6 4 Export Image Dialog 6 5 About Window Additional Features 7 1 Using the Mouse to Select 7 2 Magnifier Functionality 7 3 Navigating trees with keys and mouse wheel o 00000 ee eae File Formats Sl NeXML Giles oso sioa a paar es il oe ae Ea eke aa 8 2 Old Dendroscope files s s sa sms air a OR a aa aks S3 News IAEA BA Newick files co coros ao eee ae DE a e b Eee O aa a aS 8 5 Extended Newick format and rooted phylogenetic networks
17. X rante rat rat rat Co ica NA an Noui i guinea pig ba guinea pig orangutan orangutan 7 orangutan gibbon gibbon Y gibbor orma ae NL human es SSC mman L bonobo L bonbo NS bonobo chicken chicks chicken S Trees 6 Tree6 7 Tree7 grey seal cat harbor_seal horse a hedgehog hedgehog rhinoceros i harbor_seal cat platypus N cow platypus horse lf cow fin_whale opossum fin_whale opossum biue_ whale wallaroo wallaroo blue_whale rabbit gorila gibbon orangutan mouse guinea_pig gibbon orangutan Showing 1 Sof 8 Nodes 344 Edges 336 eightTrees nexml Dendroscope version 3 0 8alpha built 4 Apr 2011 4 Tree4 hedge grey_seal hog harbor_seal cat platypus opossum fin whale wallaroo blue_whale chicken abbi bonobo aN 7 human gibbon orangutan 8 Tree8 grey_seal cat harbor _seal rse hedgehog rhinoceros platypus cow opossum fin_whale Mo Aa whale N abot walaroo chicken bonobo human gorila orangutan guinea pig 78 of 372M 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 12
18. able commands Opening and saving files open file filename 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 save format value file filename Save data to file in the specified format possible formats nexus newick nexml exportimage file filename format PNG GIF JPG SVG PDF replace bool textasshapes bool title title Export a picture of the current tree source file filename new Choosing tree and visualization go tree first next prev last lt num gt set drawer drawer name Read commands separated by semicolons from the named file Open a new document Any selected trees are put in it Go to the first next previous or last tree or to a specific tree Set the drawer used to draw the tree Possible values RectangularPhylogram RectangularCladogram SlantedCladogram RadialPhylogram RadialCladogram CircularPhylogram CircularCladogram InnerCircularCladogram auxiliaryparameter change increment decrement Customizing the layout of a tree Adding Decrement Increment the auxiliary parameter used by some of the drawers 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 rotatesubtree Rotate all children of all selected nodes swapsubtree Swap subtree below sele
19. an Markus Franz and Regula Rupp Dendroscope An interactive viewer for large phylogenetic trees BMC Bioinformatics 8 460 2007 2 Daniel H Huson and Celine Scornavacca Dendroscope 3 a tool for drawing modifying and computing rooted phylogenetic networks In preparation e The Window gt Website item is used to go to the program website e The Window 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 Command Input item opens a window that can be used to enter a command see command tree or network manually in Newick Format e The Window Message Window item is used to open the Message window e If several program windows are opened they are listed at the end of the window menu 5 9 Toolbar For easier access of frequently used functions a Toolbar is provided The button images are self explicative and a description appears when passing on the buttons with the mouse 5 10 Context Menus A right mouse click when the index finger of the hand icon is positioned 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 when the index finger of the hand icon is positioned on an edge opens a context menu which allows to edit the edg
20. ance method hardwired softwired displayedTrees tripartition nestedLabels pathMultiplicity Calculate distances between two trees or networks compute DTL_reconciliation Calculate DTL reconciliation between two binary trees Selection and Deselection select all Select all nodes and edges select nodes all none leaves labeled Select nodes select edges all none short long threshold lt number gt Select all or none edges or all edges longer than or shorter than the given threshold select previous Select all labeled nodes as in previous window select labelednodes Select all labeled nodes select leaves Select all leaves select subnetwork Select subtree or subnetwork below node or edge select induced network Select subtree or subnetwork induced by selected nodes select LSA induced network Select subtree or subnetwork rooted at the LSA of the selected nodes select subpart Select parts of tree that are reachable from any selected node without crossing any reticulate edges select nonterminal Select all non terminal nodes and egdes select spanned Select all edges that connect any two selected nodes select root Select root select special Select all special edges select invert Invert the current selection select panels all Select all panels select panels invert Invert the selection of all panels select panels none Deselect all panels deselect all Deselect all nodes and edges deselect nodes Deselect all nod
21. bedding is computed There are four methods available here With No Optimization we do not attempt to optimize the embedding of networks The 2008 Algorithm optimizes embedding of networks using the algorithm described in Kloepper and Huson 2008 The 2009 Algorithm optimizes embedding of networks using the algorithm described in Huson 11 2009 The 2010 Algorithm optimizes embedding of networks using a new algorithm developed by Huson and Scornavacca in 2010 e The Layout gt Align Taxa item Attempts to align taxa in all selected trees or networks using an algorithm described in 19 e The Layout gt Connect Taxa item Connect all taxa of the same name in different trees or networks e The Layout gt Disconnect All item Disconnect all nodes in different trees or networks 5 7 View Menu The Views menu contains items for setting the grid scaling trees or networks using the magnifier and showing hiding labels e The e The e The e The e The e The e The e The e The e The e The View gt Set Grid item is used to set the tree or network grid dimensions View gt Less Panels item is used to lessen the number of panels in the grid View More Panels item is used to increase the number of panels in the grid View gt Show Scroll Bars item is used to show or hide scroll bars View Show Borders item is used to show or hide borders View Show Scale Bar item is used to show or hide scale bar View Zoom to
22. by saving a formatted tree as a nexml 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 gt New item opens a new document Any selected trees are put in it e The File Open item provides an Open File dialog to open one or more files containing input data The supported formats are nerml dendro tre nexus see Section 8 Note that the standard open dialog does not allow one to open more than one file under MacOS X As a work around press the shift key when selecting the File Open menu item so as to obtain an alternative file open dialog that allows one to select more than one file for opening e The File Open Recent can be used to re open a recently opened file e The File Add From File item adds trees or networks from a file to the current document e The File Enter Trees or Networks item enters trees in Newick or networks in extended Newick format 5 2 The The File Save item saves the current document in NeXML format The File gt Save As item saves the current document under a new name The File gt Export item opens the Choose output format dialog which is used to export the current trees or networks in a number of file formats see Section 8 The File Duplicat
23. cephalus _volans Ochotona_ princeps Ochotona_rufescens Ochotona_annectens Ochotona_curzoniae Ochotona_erythrotis Ochotona forresti Ochotona_himalayana Ochotona_koslowi Ochotona _ladacensis is y abaiensasnaniai ZO h O Nodes 327454 selected 1 Edges 327453 372 of 372M ncbi taxonomy tree Dendroscope version 3 0 8alpha built 4 Apr 2011 gt 885 6 4 HOTE 3 oe 4869 MSM QEECKOOKS AA eH EX Nomascus_leucogenys_leucogenys Gorila_gorila_gorila Pan_paniscus Pan_troglodytes_troglodytes Pan troglodytes_vellerosus O iy E C al Showing 1 e Nodes 327454 selected 1 Edges 327453 369 of 372M Figure 2 Part of the NCBI taxonomy showing Homo sapiens and his relatives without and with the magnifier turned on 2 G Cardona F Rossell and G Valiente Comparison of tree child phylogenetic networks IEEE ACM Transactions on Computational Biology and Bioinformatics 6 552 569 2007 3 Gabriel Cardona Merc Llabr s Francesc Rossell and Gabriel Valiente On Nakhleh s metric for reduced phylogenetic networks IEEE ACM Transactions on Computational Biology and Bioinformatics 6 4 629 638 2009 4 Gabr
24. cted node s reset labelpositions Reset all node label positions center Center the trees rotate angle number set hflip falseltrue rotatelabels percent lt integer gt creating and modifying trees add tree newick tree add file filename extract induced network extract LSA induced network extract subnetwork remove taxa selected names set unlockedgelengths true false Rotate the whole tree by the given angle in radian Flip the tree horizontally Rotate the labels of selected nodes Add the specified trees or networks in extended Newick format to the list of trees Add trees or networks from a file to the current document Extract subtree or subnetwork induced by selected nodes Extract subtree or subnetwork rooted at the LSA of the selected nodes Extract subtree or subnetwork below node or edge Remove all selected taxa if taxa selected otherwise remove named taxa Allow user to reshape tree by dragging nodes or internal edge points 19 edit edgelabels Edit the selected edge labels edit nodelabels Edit the selected node labels align trees selected or all Attempts to align taxa in all selected trees or networks set name lt name gt treeId lt tree number gt Set the name of a tree or network Algorithms compute mult2net method HOLM cluster levelk Compute a network from a multi labeled tree compute consensus method Strict Majority Loose level k network threshold lt value gt
25. e item duplicates this document The File Export Image item opens the Export Image dialog which is used to save the current network in a number of different graphics formats see Section 8 6 The File Page Setup item setups the page for printing The File gt Print item prints the network 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 Windows and Linux only Edit Menu Edit menu contains the usual edit related items The Edit gt Copy item is used to copy the current tree or network or all selected trees or networks The Edit gt Copy Image item is used to copy the current tree or network or all selected trees or networks as an image that can be pasted into another program e g PowerPoint The Edit gt Paste item is used to paste the copied trees or networks to a new tab The Edit gt Find item opens the Find tool bar which can be used to search for taxa The Edit gt Find Again item finds the next occurrence of a search string The Edit Replace item opens the Replace tool bar which can be used to replace taxon names The Edit Reroot item reroots the tree or the network at the specified nodes 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 If several nodes share
26. e 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 to scale the tree or network to fit the window or finally to show or hide scroll bars and borders 13 5 11 Status Line The Status Line 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 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 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 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 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 and Replace
27. es e The Select Select Nodes item is used to select all nodes e The Select Select Edges item is used to select all edges e The Select From Previous Window item is used to apply the selection of the previous window to the active window e The Select Deselect All item is used to deselect all nodes and edges that are currently selected e The Select gt Deselect Nodes item is used to deselect all nodes that are currently selected e The Select Deselect Edges tem is used to deselect all edges that are currently selected e The Select gt Select Labeled Nodes item is used to select all labeled nodes e The Select gt Select Leaves item is used to select all leaves e The Select gt Select Root item is used to select the root node of the tree e 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 gt 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 The advanced selection submenu contains the following items 5 4 The The Advanced Selection Select Subnetwork item is used to select the subtree or subnetwork below a selected inner node or edge The Advanced Selection gt Select Induced Network item
28. es deselect edges Deselect all edges list taxa selected List all currently selected taxa Searching show finddialog true false Show or hide find replace dialog find searchtext text target Nodes Edges all bool regex bool wholeword bool respectcase bool Find and select labels matching the given search text replace searchtext text replacetext text target Nodes Edges all bool regex bool wholeword bool respectcase bool Find and replace labels matching the given search text Collapsing and uncollapsing nodes collapse what selected complement Collapse all selected nodes or their complement collapse level lt integer gt Collapse all nodes at the given level distance from root uncollapse what all selected subtree Uncollapse all nodes all selected nodes or the whole subtree below each selected node Visualization set grid rows x cols Set the tree grid dimensions set window width num height num x num y num Set size and location of main window set layouter Unoptimized Algorithm2008 Algorithm2009 Algorithm2010 Algorithm2010Dist AlgorithmLSA Chooses the way the network embedding is computed set font name Set font by name set autolayoutlabels true false Set auto layout of labels set margin left num right num top num bottom num Set the margin around the tree set approxthreshold int Set minimum threshold for representing subtrees by approximate shapes show edgelabels true
29. false Show or hide edge labels show edgeweights true false Use the edge weights as edge labels show nodelabels true false Show or hide node labels show boarders true false Show or hide borders show scalebar true false Show or hide scale bar show scrollbars true false Show or hide scroll bars set edgeshape value Set the shape of selected edges possible values angular straight curved set nodeshape value Set the shape of selected nodes possible values rectangle oval none set radiallabels true false Set radial layout of node labels 20 set sparselabels true false set color r g b set fillcolor r g b set labelcolor r g b set labelfillcolor r g b set edgewidth num set nodesize num Scaling contract direction horizontal contract direction vertical expand direction horizontal expand direction vertical zoom selection zoom what lt contract expand fit gt Controlling the magnifier set magnifier truelfalse set magradius lt integer gt set magdisplacement lt float gt set magnifyallmode true false Adding images to nodes load imagedir lt directory name gt set imageheight lt integer gt set imagelayout lt value gt Special purpose update set dirty truelfalse set vint truelfalse set scalebar true false set prop lt name gt lt value gt tofront Other howtocite website version help keyword about clo
30. ge near the node representing the given taxon recognized formats GIF JPG JPEG BMP and PNG The Options Set 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 Next Tree item moves to the next tree The Options Previous Tree item moves to the previous tree The Options gt Go to Tree item goes to a specific tree The Options Set Tree Name item sets the name of a tree or network The advanced options submenu contains the following items 5 5 The trees The Advanced Options Extract Subnetwork item is used to extract a subtree or subnetwork below a node or edge The Advanced Options Extract Induced Network item is used to extract a subtree or subnet work induced by the selected nodes to a new file The Advanced Options Extract LSA Induced Network item is used to extract a subtree or subnetwork rooted at the LSA of the selected nodes to a new file The Advanced Options Extract Induced Restriction item is used to extract the restriction induced by the selected nodes to a new file Algorithms Menu Algorithms menu contains items for computing networks from trees and for comparing or networks The Algorithms Advanced Algorithms submenu contains additional advanced algo rithms that are probably no
31. hod 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 7 The level k based method extracts all clusters and then seeks to compute a level k network of minimum level k for the clusters The Algorithms Hybridization Network item computes all minimum hybridization networks for two rooted phylogenetic trees not necessarily binary on overlapping taxon sets using the Autumn algorithm 15 The Algorithms Hybridization Network Binary Trees item computes all minimum hybridization networks for two bifurcating trees on the same taxon set 1 The Algorithms Reroot By Hybridization Number item determines a rooting that minimizes the hybridization number given two rooted phylogenetic trees not necessarily binary on overlapping taxon sets using the Autumn algorithm 15 item The Algorithms gt Tanglegram gt i tem is used to compute a tanglegram for two trees or networks using a NeighborNet based heuristic 19 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 as it uses the Z closure method to merge partial data 14 The advanced algorithms submenu contains the following items the Advanced Algorithms Hybridization Number item is used to compute the hybridization number for
32. ic trees and networks Bioinformatics 27 13 1248 1256 2011 M A Steel S Linz D H Huson and M J Sanderson Identifying a species tree subject to random lateral gene transfer Journal of Theoretical Biology 322 81 93 2013 Leo van lersel and Steven Kelk Constructing the simplest possible phylogenetic network from triplets Algorithmica 2009 DOI 10 1007 s00453 009 9333 0 Leo van lersel Steven Kelk Regula Rupp and D H Huson Phylogenetic networks do not need to be complex using fewer reticulations to represent conflicting clusters Bioinformatics 26 12 1124131 June 2010 Chris Whidden and Norbert Zeh A unifying view on approximation and fpt of agreement forests In Steven Salzberg and Tandy Warnow editors Algorithms in Bioinformatics volume 5724 of Lecture Notes in Computer Science pages 390 402 Springer Berlin Heidelberg 2009 27 Index 2008 Algorithm 11 2009 Algorithm 11 2010 Algorithm 12 About 13 16 Add From File 5 Advanced Algorithms 9 Advanced Algorithms gt Displayed Trees Dis tance 10 Advanced Algorithms gt DTL Reconciliation 10 Advanced Algorithms Hardwired Cluster Dis tance 10 Advanced Algorithms Hybridization Number 10 Advanced Algorithms Hybridization Number Binary Trees 10 Advanced Algorithms gt Nested Labels Distance 11 Advanced Algorithms gt Path Multiplicity Dis tance 11 Advanced Algorithms rSPR Distance Binary Trees 10 Advanced Alg
33. iel Cardona Francesc Rossell and Gabriel Valiente Extended Newick It is time for a standard representation of phylogenetic networks BMC Bioinformatics 9 532 2008 5 J P Doyon C Scornavacca K Yu Gorbunov G J Sz ll si V Ranwez and V Berry An efficient algorithm for gene species trees parsimonious reconciliation with losses duplications and transfers In Research in Computational Molecular Biology Proceedings of the 14th In ternational Conference on Research in Computational Molecular Biology RECOMB volume 6398 of LNCS pages 93 108 Springer 2010 24 editedTree nexml 2 Dendroscope version 3 0 8alpha built 4 Apr 2011 gt e858 A HOJE f ee QPo HEM QEESXDORO LA EH wallaroo opossum platypus hedgehog Format editedTree nexml 2 Dendroscope Font Helvetica 15 Size 11 7 O Bold O Italic harbor_seal Swatches HSB RGB dl Y Line Color rr cat O Fill Color horse rhinoceros Label Color cow fin_whale C Label Fill Color blue_whale a Random Colors Invisible Again rabbit Node size 2 v Node shape square arat Edge width Edge Style angular Show Labels V Rotate Node Labels amp Left Right LC 95 Close puinea_ply 7 orangutan L gibbon gorilla human bonobo
34. ioinformatics 1 1 13 23 2004 17 Luay Nakhleh A metric on the space of reduced phylogenetic networks IEEE ACM Trans actions on Computational Biology and Bioinformatics 99 RapidPosts 2009 26 18 19 20 21 22 23 a na phyB_rbcL tanglegram nexml 4 Dendroscope version 3 0 8alpha built 4 Apr 2011 lt gt aapa i AED S ee Qeo MAM QEE lt KOKO LMA EG al 12 miscanthus _____miscant thus chasmanthi chasmanthi L thysanolae thysanolae Phragmites phragmites moiinia molinia eragrostis eragrostis danthonia danthonia 1 aristida aristida oe ee 9 triticum triticum S L bromus bromus L avena avena oryza oryza p pseudosasa pseudosasa r chusquea chusquea lithachne lithachne flagellar flagellari L joinvillea joinvilea anomochloa anomochloa puelia puelia pennisetum pennisetum zea zea Showing 1 20f2 gt Nodes 98 Edges 104 539 of 745M Figure 5 A tanglegram for two phylogenetic networks H A Schmidt Phylogenetic trees from large datasets PhD thesis Heinrich Heine Universitat Dusseldorf 2003 C Scornavacca F Zickmann and D H Huson Tanglegrams for rooted phylogenet
35. is used to select a subtree or subnet work induced by the set of currently selected nodes The Advanced Selection gt Select LSA Induced Network item is used to select the subtree or subnetwork rooted at the LSA of the selected nodes The Advanced Selection Select Spanned Edges item is used to select all edges spanned by the set of currently selected nodes Options Menu Options menu contains items for collapsing nodes and extracting subtrees The Options Advanced Options submenu contains some advanced options that are probably not of general interest The Options Collapse item enables to collapse subtrees or subnetworks below the specified nodes The former subtrees or subnetworks are replaced by rectangles The Options Uncollapse item is used to uncollapse expand the selected collapsed subtrees or subnetworks The Options Uncollapse Subtree item is used to uncollapse expand all collapsed subtrees or subnetworks below the specified nodes The Options Collapse Complement item is used to collapse all subtrees or subnetworks except the currently selected part of the tree or subnetwork The Options Collapse at Level item is used to collapse all subtrees or subnetworks at the specified level from the root The Options gt Load Taxon Images item is used to specify a directory containing image files Dendroscope tries to match taxon names to the names of images files and for each match found Dendroscope shows the ima
36. ment 8 command 19 Command Input 13 19 Command input 19 command line 21 command line mode 22 Command line Syntax 13 Connect Taxa 12 Copy 6 Copy Image 6 curved edges 14 28 default font setting 14 Delete Taxa 7 Dendroscope About 13 16 Dendroscope_macos_3 3 2 dmg 4 Dendroscope_unix_3 3 2 sh 4 Dendroscope_windows_3 3 2 exe 4 Deselect All 7 Deselect Edges 7 Deselect Nodes 7 Disconnect All 12 Displayed Trees Distance 10 Draw Circular Cladogram 5 11 Draw Circular Phylogram 5 11 Draw Inner Circular Cladogram 5 11 Draw Radial Cladogram 5 11 Draw Radial Phylogram 5 11 Draw Rectangular Cladogram 5 11 Draw Rectangular Phylogram 5 11 Draw Slanted Cladogram 5 11 DTL Reconciliation 10 Duplicate 6 edge labels 12 edge width 14 Edit 6 Edit Copy 6 Edit gt Copy Image 6 Edit Delete Taxa 7 Edit gt Find 6 14 Edit gt Find Again 6 Edit Format 5 7 14 Edit Paste 6 Edit Reorder Subtrees 7 Edit Replace 6 15 Edit Reroot 6 Edit Rotate Subtrees 6 Edit Swap Subtrees 6 Edit Unlock Edge Lengths 7 Enter Trees or Networks 5 exact method 10 Export 5 6 Export Image 5 6 15 Extended Newick 17 Extract Induced Network 9 Extract Induced Restriction 9 Extract LSA Induced Network 9 29 Extract Subnetwork 9 File 5 File Add From File 5 File gt Close 6 File gt Duplicate 6 File gt Enter Trees or Networks 5 File gt Expo
37. oaded from tre Newick format or nexus files or entered manually Rooted phylogenetic networks can be entered and visualized using the Extended Newick format 4 The program permits the computation of consensus trees from a set of input trees The program also permits the computation of rooted phylogenetic networks among others cluster networks 11 galled networks 12 minimum networks 22 and hybridization networks 1 15 from a set of input trees It provides several tree manipulating functions like rerooting subtree rotating tree flipping and formatting features like renaming coloring or resizing edges nodes and labels 3 Obtaining and Installing the Program Dendroscope is written in Java and requires a Java runtime environment version 1 7 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_3 3 2 exe provides an installer for Windows e Dendroscope_macos_3 3 2 dmg provides an installer for MacOS e Dendroscope_unix_3 3 2 sh provides a shell installer for Linux and Unix Alternatively Dendroscope will be available as Java Webstart application from http ab inf uni tuebingen de data software dendroscope webstart If you need information concerning Java Webstart go to http java sun com products javawebstart 4 Getting
38. ode but should not be used interactively To prevent windows from opening or to use the command line mode on a server please use the linux virtual frame buffer command as shown here xvfb run auto servernum server num 1 Dendroscope g 12 Examples In this section we illustrate some of the features of Dendroscope 12 1 Basic tree view Figure 1 shows the eight views possible with Dendroscope for the same phylogenic tree of mammal species 12 2 Additional tree view features Figure 2 illustrates the action of the Magnifier on part of the NCBI taxonomy tree close to Homo sapiens 12 3 Editing trees Figure 3 demonstrates some of the editing possibilities present in Dendroscope 12 4 Constructing rooted phylogenetic networks Figure 4 depicts two phylogenetic trees from the Poaceae dataset from the Grass Phylogeny Working Group 6 and the 4 hybrid networks computed from these trees by the method presented in 1 22 gt anaia E 1 Tree1 353300 94953 Mel QEESADORAO 444 20 2 Tree2 3 Tree3 walaroo wallaroo g Wallaroo opossum opossum N opossum platypus platypus platypus hedgehog hedgehog hedgehog harbor_seal grey seal rise seal grey_seal cat cat cs harbor_seal Pa grey_seal d La cat horse horse horse rhinoceros rhinoceros EN rhinoceros in he fin_whale fin_whale L Xm whale Le wale atado L bue wale rabet a Xx
39. orithms gt Simplistic 11 Advanced Algorithms Softwired Cluster Dis tance 10 Advanced Algorithms gt Tripartition Distance 11 Advanced Options 8 Advanced Options gt Extract Induced Network 9 Advanced Options gt Extract Induced Restric tion 9 Advanced Options gt Extract LSA Induced Net work 9 Advanced Options gt Extract Subnetwork 9 Advanced Selection 7 Advanced Selection Select Induced Network 8 Advanced Selection Select LSA Induced Net work 8 Advanced Selection Select Spanned Edges 8 Advanced Selection Select Subnetwork 8 Algorithms 9 Algorithms Advanced Algorithms 9 Algorithms Hybridization Network 10 Algorithms Hybridization Network Trees 10 Algorithms gt Loose Consensus 9 Algorithms gt LSA Consensus 9 Algorithms gt Majority Consensus 9 Algorithms gt Network Consensus 9 Algorithms gt Network for Multi Labeled Tree 10 Algorithms gt Primodial Consensus 9 Algorithms gt Reroot By Hybridization Number 10 Algorithms Strict Consensus 9 Algorithms gt Tanglegram gt i 10 Align Taxa 12 All Panels 7 angular edges 14 apply a command 19 apply to all trees and networks 19 Binary Batik 23 BMP 18 Case sensitive 14 Choose output format 6 circle nodes 14 circular 16 citing the program 3 click selection 16 Close 6 15 cluster network 10 cluster based method 10 Collapse 8 Collapse at Level 8 Collapse Comple
40. plistic algorithm 11 Softwired Cluster Distance 10 softwired representation 10 Sparse Labels 12 square nodes 14 Status Line 14 straight edges 14 Strict Consensus 9 strict consensus 9 SVG 18 Swap Subtrees 6 tanglegram 10 Toolbar 13 Tripartition Distance 11 Type setting conventions 3 Uncollapse 8 Uncollapse Subtree 8 Unix 4 Unlock Edge Lengths 7 Unselect All 15 Use Magnifier 5 12 16 View Fully Contract 12 View Fully Expand 12 View Label Edges By Weights 12 View Less Panels 12 View Magnify All Mode 12 View More Panels 12 View Radial Labels 12 View Reposition Labels 12 View Set Grid 12 View Show Borders 12 View Show Edge Labels 12 View Show Node Labels 12 View Show Scale Bar 12 View gt 5Show Scroll Bars 12 View Sparse Labels 12 View Use Magnifier 5 12 16 View Zoom to Fit 12 Views 12 virtual frame buffer command 22 Website 13 Webstart application 4 Whole words only 14 Window 13 Window About 13 16 Window Command Input 13 19 Window Command line Syntax 13 Window How to Cite 13 Window Message Window 13 15 Window Set Window Size 13 Window Website 13 Windows 4 Zoom to Fit 12 32
41. program and its authors 7 Additional Features 7 1 Using the Mouse to Select Nodes edges and labels can also be selected by clicking on them with the index finger of the hand icon If the left mouse click is press for 2 seconds or shift clicking an arrow appears dragging the mouse it is possible to perform a 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 portions 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 b
42. program in command line mode and typing or piping commands to the program via the console The Command input window has a field for entering commands a cancel button and two different apply buttons The Apply button applies the entered command to the current tree or network whereas the Apply to Every Tree in File button applies the entered command to all trees and networks in the current file each one separately Use this button with care To start Dendroscope in command line mode use the option g For example under MacOS X type installation dir Dendroscope Dendroscope app Contents MacOS JavaApplicationStub g in a terminal shell To make things easier in the command line version only one file is opened at the time When new trees or networks are computed the file is emptied and filled with the newly computed trees and networks To apply a set of commands to all trees and networks in the current file in the command line version use the syntax apply all begin lt command gt lt command gt apply all end Note that the Apply to All syntax should only be used for commands that change the trees or networks e g for computing the consensus network or changing the drawer for all trees in the file and not for commands that change transient aspects of the visualization such as zoom factor edges nodes selection etc Also it is pointless to use a command such as open file or add file in this context Here is a summary of all avail
43. rees in this format 8 4 Newick files Dendroscope can read Newick files and can export trees in this format 8 5 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 proposed by 4 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 end of node labels These special labels are of the form HI 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 17 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 b H1 c H1 Copy and paste this string into a Dendroscope window to see the corresponding network In Dendroscope quite everything that can be done with a rooted tree can also be done with a rooted phylogenetic network 8
44. rt 5 6 File gt Export Image 5 6 15 File gt New 5 File gt 0Open 5 File gt 0Open Recent 5 File gt Page Setup 6 File Print 5 6 File gt Quit 6 File gt Save 6 File gt Save As 5 6 Find 6 14 Find Again 6 Find All 15 Find First 15 Find Next 15 font family 14 font size 14 font style 14 Format 5 7 14 Format Panel 14 From Previous Window 7 Fully Contract 12 Fully Expand 12 galled network 10 GIF 18 Global 14 Go to Tree 9 graphics formats 18 Hardwired Cluster Distance 10 hardwired representation 10 How to Cite 13 How to cite 3 Hybridization Network 10 Hybridization Network Binary Trees 10 Hybridization Number 10 Hybridization Number Binary Trees 10 1 10 Image Position 9 Invert Panels 7 Invert Selection 8 JPEG 18 key bindings 16 Label Edges By Weights 12 Ladderize Left 11 Ladderize Random 11 Ladderize Right 11 Layout 11 Layout Align Taxa 12 Layout Connect Taxa 12 Layout Disconnect All 12 Layout Draw Circular Cladogram 5 11 Layout Draw Circular Phylogram 5 11 Layout Draw Inner Circular Cladogram 5 11 Layout Draw Radial Cladogram 5 11 Layout Draw Radial Phylogram 5 11 Layout Draw Rectangular Cladogram 5 11 Layout gt Draw Rectangular Phylogram 5 11 Layout Draw Slanted Cladogram 5 11 Layout gt Ladderize Left 11 Layout Ladderize Random 11 Layout Ladderize Right 11 Layout Network Layout
45. s obtained in part by using Dendroscope then we require that you acknowledge this by citing the program as follows e Daniel H Huson and Celine Scornavacca Dendroscope 3 An interactive tool for rooted phy logenetic trees and networks Systematic Biology 2012 http sysbio oxfordjournals org cgi content abstract sys0627i jkey ZCxPRbYt74aQ JhR amp keytype ref software freely available from www dendroscope org This manual is based on the user manual for Dendroscope 1 which was written by Daniel H Huson Daniel C Richter Christian Rausch and Regula Rupp The source files for Dendroscope can be found here http danielhuson github io dendroscope3 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 overview of its features There are 8 different tree views available e g phylogram cladogram or radial views Its novel navigational features facilitate the analysis of large trees It provides several tree manipulating functions like rerooting subtree rotating tree flipping and formatting features like renaming coloring or resizing edges nodes and labels A comprehensive set of export formats for the generation of images is available User formatted trees can be saved as a NeXML project file or as nexus or Newick tree files Tree structures single or multiple can be l
46. se quit Here is an example Set sparse layout of node labels in which labels that would overlap others are not shown Set the color of all selected nodes and edges Set the fill color of selected nodes Set the label color of all selected nodes and edges Set the label fill color of selected nodes and edges Set the line width of all selected edges Set the size of all selected nodes Contract horizontally Contract vertically Expand horizontally Expand vertically Zoom to current selection of nodes Fully contract fully expand or zoom to fit the whole tree or network in the window Turn magnifier on or off Set magnifier radius Set magnifier displacement power Set the magnifier all mode Load image files from named directory Images are placed next to taxa of same name recognized formats GIF JPG JPEG BMP and PNG Set the height of the images associated with all selected nodes Set the layout used for images possible values north south east west radial Update the trees Set the dirty status of a document Set show version in window title mode Set show scalebar mode Set the boolean value of a named property Bring window to front How to cite the program Go to the program website List version info List this help or list help on given keyword List information about Dendroscope Close the window Quit the program open file installation dir Dendroscope examples trees new select taxa AE007869
47. t of general interest The Algorithms Strict Consensus item is used to compute the strict consensus of a set of trees The Algorithms gt Loose Consensus item is used to compute the loose consensus of a set of trees The Algorithms Majority Consensus item is used to compute the majority consensus of a set of trees The Algorithms LSA Consensus item is used to compute the LSA consensus of a set of trees 13 The Algorithms Primodial Consensus item is used to compute the primodial con sensus of a set of trees 20 The Algorithms 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 11 that shows the clusters in a hardwired representation a galled network 12 that represents the clusters in a topologically restricted softwired representation ora minimum network that attempts to represent the clusters in a network of minimum level as described in 22 The Algorithms 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 based met
48. two rooted trees using the Autumn algorithm 15 Trees need not be binary and need not have identical taxon sets the Advanced Algorithms Hybridization Number Binary Trees item is used to compute the hybridization number for two selected rooted binary trees on the same taxon set 1 the Advanced Algorithms gt rSPR Distance Binary Trees item is used to compute the rSPR distance for two selected rooted binary trees on the same taxon set 23 the Advanced Algorithms DTL Reconciliation item is used to calculate the DTL reconciliation between two binary trees 5 the Advanced Algorithms gt Hardwired Cluster Distance item is used to calculate the hardwired cluster distance between two trees or networks 13 the Advanced Algorithms Softwired Cluster Distance item is used to calculate the softwired cluster distance between two trees or networks 13 the Advanced Algorithms gt Displayed Trees Distance item is used to calculate the displayed trees distance between two trees or networks 13 10 5 6 The the Advanced Algorithms Tripartition Distance item is used to calculate the tripartition distance between two trees or networks 16 the Advanced Algorithms Nested Labels Distance item is used to calculate the nested labels distance between two trees or networks 3 17 the Advanced Algorithms Path Multiplicity Distance item is used to calculate the path multiplicity distance between two trees or networks 2
49. uttons 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 Press the shift key to zoom the graph in horizontal direction e Rotating For circular and radial drawings use the shift key and left and right arrow keys to rotate the tree 16 Alternatively use the arrow keys to scroll the tree or network or additionally press the shift key to zoom the graph in horizontal or vertical direction zoom not available in this way for circular and radial drawings Use the alt and control keys for acceleration 8 File Formats Dendroscope uses the NeXML file format to store the data of the modified and or formatted tree or network By convention we use the suffix nerml for NeXML files 8 1 NeXML files Dendroscope saves trees in a simple text based format with the file extension nexml 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 line widths etc are lost 8 2 Old Dendroscope files For backward compatibility this version of Dendroscope can still open dendro files see the old version of this manual 8 3 Nexus files Dendroscope can read a Nexus file that contains a Nexus trees block and can export t
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