User Manual for MetaSim V0.9.5
Contents
1. 0 20 20 02 eee eee eee 9 Run Simulation Window 10 Find Window 11 Population Sampler 11 1 Usage of Population Sampler 11 2 Naming Convention 12 Taxonomy Editor 12 1 Usage 2 12 2 Setting the Number of Genomes 00002 eee eee ee 12 3 File Menu Taxonomy Editor 11 12 12 13 13 13 13 13 14 14 15 15 16 17 20 20 20 21 21 21 12 4 Edit Menu Taxonomy Editor 2 coe cesse roe natua a 54 See eee eee 23 12 5 Select Men Taxonomy Editor ao caa saa tuca matig o ee ee A A 23 12 6 Options Menu Taxonomy Editor 0 0002 eee eee 24 12 7 View Menu Taxonomy Editor 0 0 00 a 24 126 Toolbar Taxonomy Editor lt oae pba Be eRe he RO OE A 25 13 Command Line Options 25 14 File Formats 28 14 1 FASTA header of Output Files 200 00 a 29 15 Examples 29 References 30 Index 31 1 Introduction Disclaimer This software is provided AS IS without warranty of any kind This is develop mental code and we make no pretension as to it being bug free and totally reliable Use at your own risk We will accept no liability for any damages incurred through the use of this software Use of the MetaSim is free however the program is not open source How to cite If you publish results obtained in part by using MetaSim then we require that you acknowledge this by citing the program as follows e D C Richter F Ott A F Auch R Schmid and D H Huson MetaSi2. Get Taxon IDs NCBI ftp 10 12 Database Get Taxon IDs by GI 10 12 Database Import Files 5 9 12 Database Remove Selected Sequences 9 Database Reset SQL Query 10 13 Database Set SQL Query 10 13 22 Database Show Database 5 9 12 Database Show Hash Key 10 Decrease Font Size 9 Deletion Error Rate 17 DELETION_ERROR 18 Deselect All 23 Deselect Edges 24 Deselect Nodes 24 Disable Selected Sequences 10 Disclaimer 3 DNA Clone Size Distribution Type 16 edge labels 25 Edit 8 Edit Selected Preset 11 15 Edit gt Copy 9 23 Edit gt Cut 8 Edit Find 9 11 20 23 25 Edit Find Again 9 23 Edit Format 23 25 Edit Paste 9 Edit Preferences 9 12 Edit gt Taxonomy Editor 9 Edit Text Editor 9 Empirical Error Model 17 Empirical Error Rates 18 Enable Selected Sequences 9 Error Model 15 Error Model Configuration 16 Error Rate at Read End 17 Error Rate at Read Start 17 Evolve Button 21 Evolve Selected Sequences 10 21 Exact Error Model 20 example taxon profilel mprf 29 example taxon profile2 mprf 30 example_project_l msim 30 examples 29 Expand view horizontally 25 Expand view vertically 25 Expected Read Length 16 Export Image 23 25 31 Export Selected Preset 11 15 Export Selected Sequences 9 13 21 File 8 File Close 8 23 File gt Export Image 23 25 File New Project 5 8 File Open 8 11 File gt Open Taxonomy Editor
3. Acaryochloris marina MBIC11017 OFF_0003 taxon0010 Acaryochloris marina MBIC11017 OFF_0100 taxon0087 Offspring sequences are not visualized in the Taxonomy Editor Selecting Offspring Sequences in Database The naming convention is useful if one wishes to remove or disable all offspring sequences in the database Therefore the SQL query tool Database Set SQL Query can be used SELECT enabled gi taxid name circular copies length key FROM SEQUENCES WHERE name like OFF ORDER BY name 12 Taxonomy Editor To facilitate the design of taxon profiles MetaSim provides an interactive Taxonomy Editor It is based on the NCBI taxonomy and visualizes every species genome sequence from the database as a leaf in a tree Genome sequences in the database must be assigned a taxon id Otherwise the taxonomy editor will not work properly 12 1 Usage The Taxonomy Editor window is opened using the Taxonomy Editor button on the bottom right of the main panel This button is enabled if the user has selected a empty taxon profile from the Project Tree Once the taxonomy editor is initialized a taxonomic tree is displayed embedding all sequences with an unique taxon id from the internal database To set the abundance values right click on a node and select Set Number of Genomes from the context menu After that one can save these settings to the current opened taxon profile or one can create a new taxon profile After the sa
4. The Project Export Selected Preset writes all parameters of a selected preset to a file mprs This file can be imported again by using Project Import Presets This can be useful for sharing presets between different projects The Project Run Simulation item opens the Run Simulation Window The user can select from the available presets and simulation settings Finally the simulation can be started The Project Run With Selected Preset item opens the Run Simulation Window In contrast to Project Run Simulation the selected preset is already set The Project Run For Selected Profile item opens the Run Simulation Window In contrast to Project Run Simulation the selected taxon profile is already set Window Menu The Window How to cite item gives instructions on how to cite the program The Window About item shows information about the version of MetaSim When the program is run under MacOS this menu item appears in the MetaSim menu MetaSim Menu Under MacOS there is an additional standard menu associated with the program called the MetaSim menu As usual this contains the Window About and File Quit menu items 5 10 Tool Bar The Main Window provides a tool bar containing buttons that provide short cuts to some of the menu items associated with the window These are the File Open File Save As Edit gt Find and Project Run Simulation items 6 Database Functionality The internal Database rep
5. B Makhijani K E McDade M P McKenna E W Myers E Nickerson J R Nobile R Plant B P Puc M T Ronan G T Roth G J Sarkis J F Simons J W Simpson M Srinivasan K R Tartaro A Tomasz K A Vogt G A Volkmer S H Wang Y Wang M P Weiner P Yu R F Begley and J M Rothberg Genome sequencing in microfabricated high density picolitre reactors Nature 437 7057 376 380 2005 es G Udny Yule A mathematical theory of evolution based on the conclusions of Dr J C Willis Philosophical Transactions of the Royal Society of London Ser B Biol Sci 213 21 87 1925 30 Index h 25 MetaSim cmd joption s 25 mconf 29 mprf 28 msim 28 ir30 1 29 18 14 100 14 A T G C 18 About 11 Acaryochloris marina MBIC11017 22 Add Files 10 Backward 20 Base Substitution Rate 18 Case Sensitive 20 Close 8 21 23 Collapse 24 Collapse at Level 24 Collapse Complement 24 command line options 25 Compress Output gzip 16 Contract view horizontally 25 Contract view vertically 25 Copy 9 23 Create New Preset 7 10 15 Create Taxon Profile From Selection 5 Create Taxon Profile from Selection 9 13 Cut 8 Database 9 11 Database Create Taxon Profile from Selection 9 13 Database Disable Selected Sequences 10 Database Enable Selected Sequences 9 Database Evolve Selected Sequences 10 21 Database Export Selected Sequences 9 13 21 Database
6. The Database Remove Selected Sequences item removes selected sequences from the database The Database Create Taxon Profile from Selection item can be used to create a new taxon profile based on selected entries in the database See Section 7 1 The Database Export Selected Sequences item can be used to export selected se quences into a multi fasta file The Database Enable Selected Sequences enables the selected sequence Enabled sequences are used in the process of read simulation 5 7 The The Database Disable Selected Sequences disables the selected sequence Disabled sequences in the database are not considered commented out in taxon profiles Likewise they are not considered for the simulation of reads The Database Evolve Selected Sequences item opens the Population Sampler win dow It can be used to generates a set of evolved mutated offsprings derived from the selected sequences The Database Get Taxon IDs by GI can be used to infer taxon ids from GIs for each existing sequence in the database Therefore a special mapping file is needed See Section 6 1 The Database Get Taxon IDs NCBI ftp can be used to infer taxon ids from a remote file for each existing sequence in the database Therefore a ftp network connection is established See Section 6 1 The Database Show Hash Key item is used to add another column to the database named key It is the internal unique key that distinguishes seq
7. algorithm generates a signal trace This does not affect the results Currently the signal trace is only used internally Simulator Options Number of Threads In case of running MetaSim on a multiprocessor machine select the number of threads to distribute the computation Generate FASTA Output If unchecked the program will just simulate the generation of reads without writing results to a file The result log displays the simulation results Compress Output gzip Automatically compresses the multifasta file using gzip Use Uniform Sequence Weights If unchecked disables weighting of sequences by sequence length and number of per genome copies Merge All Files Into a Single Taxon Profile If checked merge all files in the profile folder into a single taxon profile Output will be one multifasta file If unchecked output will be one multifasta file per taxon profile Sanger Parameter Settings Primary Configuration see Primary Configuration of 454 parameter settings 16 e Error Model Configuration Read Length Distribution Normal Uniform Distribution of read sequence length Mean Mean length of read sequence Second Parameter Standard deviation of mean read length Mate Pair Probability Value betw 0 and 1 0 means no mate pair Error Rate at Read Start Value between 0 00 and 1 00 Error Rate at Read End Value between 0 00 and 1 00 Insertion Error Rate Value between 0 00 and 1 00 Deletion Error Rate Value between
8. in the Main Panel use Database Show Database or click on the Database item in the Project Tree Several column headers are shown 1 enabled enables disables a genome sequence Only enabled sequences are used for the read sampling 2 gi NCBI s gi number of the genome sequence 3 taxid NCBI s taxonomy id 1 if not assigned 4 name name of the organism genome sequence 5 circular does the sequence have a circular topology 6 copies copy number of the sequence 7 length length of the sequence base pairs You can click on each column header to sort the table To be able to use the Taxonomy Editor each sequence should be assigned a unique taxonomy id 1 This is explained in Section 6 1 12 6 3 Searching the Database The database can be searched by using standard SQL syntax For searching use Database Set SQL Query Example SELECT enabled gi taxid name length FROM sequences WHERE length gt 3000000 ORDER BY length To reset the SQL query ie to to see all present genome sequences in the database use Database Reset SQL Query Additionally use the Find Window 6 4 Exporting Sequence Files To export sequences to multi fasta file s fna select one or more entries in the database and use the Database Export Selected Sequences Alternatively right click on the set of selected entries and use Export Selected Sequences 7 Taxon Profiles A Taxon Profile determines the compositio
9. text The Edit gt Find item opens the Find Window which can be used to search the database taxon profiles and the message panel The Edit Find Again finds the next occurrence of a search string The Edit Preferences opens a submenu with the following items Preferences Set Database Location can be used to set the location of the database to a new path in the file system The default path is the installation directory The Preferences Set Defaults opens the simulation settings window to enable the user to determine default values e g number of reads These values will appear for each new simulation preset by default Ifthe Preferences Show Message Panel is checked the message panel will be visible otherwise it will be hidden The Preferences Increase Font Size and Preferences Decrease Font Size items change the font size of the database The database has to be selected first to enable these menu items The Edit Taxonomy Editor items open the Taxonomy Editor for a selected taxon profile The Edit gt Text Editor items open the text editor for a selected taxon profile in the Main Panel Database Menu Database menu contains the following database related items The Database Show Database item activates the database and displays it in the main panel The Database Import Files item opens a file dialogue to import gzipped fasta files with genome sequences for the database See Section 6 1
10. the common real world situation that many different but closely related strains of a lineage coexist in the same habitat The resulting data sets can be used to plan and design metagenome studies and for evaluation and improvement of metagenomic software tools and assembly algorithms This document provides both an introduction and a reference manual for MetaSim 2 Getting Started This section describes how to get started First download an installer for the program from www ab informatik uni tuebingen de software metasim see Section 3 for details Upon first startup of the program the internal database does not contain any genome sequences To import the necessary files see Section 6 1 Alternatively to import an individual genome sequence as multi fasta file use the Database Import Files item Once sequences are loaded into the database create a new project using File New Project After this the source genome sequences have to be selected for simulation Therefore a Taxon Profile containing all desired sequences has to be created Click on the Database Show Database to display the content of the databse in the main panel Then select the sequence entries from the database Linux Win user left click hold down ctrl key Apple Users left click hold down cmd key Right click on the selected entries in the database view and use the Create Taxon Profile From Selection item After saving the file as mprf file this profile
11. 0 00 and 1 00 e Simulator Options see Simulator Options of 454 parameter settings 8 3 Empirical Error Model Parameter Settings As an additional feature MetaSim includes an Empirical Error Model that allows the incorpora tion of user defined error statistics for the generation of read sequences As default configuration the programs comes with an error model based on Illumina s sequencing technology This error model is derived from empirical studies It is based on mappings error curves that assign error rates to base positions see Fig 1 for an example 0 05 0 04 0 03 0 02 ee 0 01 t t t t t t gt 5 10 15 20 30 35 N or Figure 1 Probability curve of substition errors for 36bp reads x axis read position y axis error rate Each mapping has three parameters the last two are optional e type of error e base at position where the error occurs and 17 e base preceding the position where the error occurs In addition in case of a substitution error the user can specify the probability of integrating a particular base depending on the type of the base at the error positions and the preceding base Instructions for creating individual Empirical Error Models An empirical error model is a text based file mconf It can be created with any text editor Lines starting with are ignored There is only one file for all error model settings First of all the Base Substitutio
12. 10 13 Revert 8 Run For Selected Profile 11 Run Simulation 5 11 20 Run Simulation Window 20 Run With Selected Preset 11 Save 8 Save As 7 8 11 Save Taxonomy Profile 23 Save Taxonomy Profile As 23 Scale Standard Deviation with Square Root of Mean 16 Scroll to Selection 24 Second Parameter 16 Select 23 Select All 23 Select Edges 23 Select Leaves 24 Select Nodes 23 Select Subtree 24 Select Deselect All 23 Select Deselect Edges 24 Select Deselect Nodes 24 Select Invert Selection 24 Select List Selected Taxa 24 Select Scroll to Selection 24 Select Select All 23 Select Select Edges 23 Select Select Leaves 24 Select Select Nodes 23 Select Select Subtree 24 Set Database Location 9 Set Defaults 9 Set Number of Genomes 22 24 Set SQL Query 10 13 22 Show Database 5 9 12 Show Edge Labels 25 Show Hash Key 10 Show Message Panel 9 Show Node Labels 24 Signal Std Deviation Multiplier 16 Simulator Options 16 Sparse Labels 25 Std Deviation for Negative Flow Signals 16 SUBSTITUTION_ERROR 18 19 SUBSTITUTION ERROR X Y 19 taxid 14 33 Taxon Profile 13 Taxonomy Editor 9 22 Text Editor 9 13 Toolbar 25 Tree File 21 Uncollapse 24 Uncollapse Subtree 24 Unix 5 6 Use Magnifier 24 25 Use Uniform Sequence Weights 16 View Fully Contract 24 25 View Fully Expand 24 25 View Hide Edge Labels 25
13. 23 File Print 8 23 25 File Quit 8 11 23 File gt Recent Projects 8 File gt Revert 8 File Save 8 File Save As 7 8 11 File gt Save Taxonomy Profile 23 File Save Taxonomy Profile As 23 Find 9 11 20 23 25 Find Again 9 23 Find All 21 Find Window 20 First 21 Flow Cycles 16 Format 23 25 Forward 20 forward 21 Fully Contract 24 25 Fully Expand 24 25 Generate FASTA Output 16 Generate Signal Trace 16 Get Taxon IDs NCBI ftp 10 12 Get Taxon IDs by GI 10 12 gi 14 Global 21 Hide Edge Labels 25 Hide Node Labels 24 How to cite 3 11 Illumina s sequencing technology 17 illumina error model mconf 19 29 Import Files 5 9 12 Import Presets 11 15 Increase Font Size 9 Insertion Error Rate 17 INSERTION_ERROR 18 interchange simulation settings 15 Invert Selection 24 Jukes Cantor Model Alpha 21 key 10 Linux 5 6 List Selected Taxa 24 Load 19 MacOS 5 6 Main Panel 8 Main Window 7 Mate Pair Probability 16 Mate Pair Read Length 16 Mean 16 Mean Negative Flow Signal 16 Merge All Files Into a Single Taxon Profile 16 Message Panel 8 MetaSim 11 MetaSim cmdline 5 MetaSim linux 0 9 5 rpm 5 MetaSim macos 0 9 5 sit 5 MetaSim_unix_0 9 5 sh 5 MetaSim windows 0 9 5 exe 5 name 14 New Project 5 8 New Taxon Profile 7 10 Next 21 Node Create New Preset 7 Node New Taxon Profile 7 Number of Flow Cycles 16 Number of
14. 950 first base 0 00675296642376962 0 05190994307855664 last base Likewise 48 mappings are possible to create Note In case an equal mapping has been defined before in the file only the last one is considered This can be useful if first SUBSTITUTION_ERROR defines a default substitution rate for all bases and then SUBSTITUTION ERROR X Y specifies error rates for base Y following base X Settings in configuration Window Once all error probabilities are listed in a mconf file this file can be loaded into MetaSim e Primary Configuration see Primary Configuration of 454 parameter settings e Error Model Configuration Click the Load button to import an error model text based file ending mconf After the import the main header that are defined in the error model are summarized and displayed in the text box below For an example load the default error model based on Illumina reads 36bp by choosing the file illumina error model mconf in the examples folder e Simulator Options see Simulator Options of 454 parameter settings Outlook Due to its abstract definition the empirical error model is suitable for integrating upcoming se quencing technologies We are very interested in further empirical models of other technologies If you like to provide your error models send them to huson informatik uni tuebingen de We will provide them on our MetaSim homepage for other users 19 8 4 Exact Model Parameter Setting
15. Leaves 21 Number of Reads or Mate Pairs 15 Number of Threads 16 Offsprings 21 Open 8 11 Open Taxonomy Editor 23 Options 24 Options Collapse 24 Options Collapse at Level 24 Options Collapse Complement 24 Options Set Number of Genomes 22 24 Options Uncollapse 24 Options Uncollapse Subtree 24 Paste 9 Population Sampler 21 Preferences 9 12 Preferences Decrease Font Size 9 Preferences Increase Font Size 9 Preferences Set Database Location 9 Preferences Set Defaults 9 Preferences Show Message Panel 9 preset configuration 15 Preset Name 15 Primary Configuration 15 Print 8 23 25 Project 10 Project File 28 Project Tree 7 Project Add Files 10 Project Create New Preset 10 15 Project Edit Selected Preset 11 15 Project Export Selected Preset 11 15 Project Import Presets 11 15 Project New Taxon Profile 10 Project Reload Selected Profile 10 Project Remove Selected Files 10 Project Rename Project 10 Project Run For Selected Profile 11 Project Run Simulation 5 11 20 Project Run With Selected Preset 11 Quit 8 11 23 130 1 29 rinr of readj jindexj 29 Read Length Distribution 17 Recent Projects 8 Red Exclamation Mark 13 Regular Expression 20 Reload Selected Profile 10 13 Remove Linker Sequence From Output 16 Remove Selected Files 10 Remove Selected Sequences 9 Rename Project 10 Reset SQL Query
16. User Manual for MetaSim V0 9 5 Daniel C Richter Felix Ott Alexander F Auch Ramona Schmid and Daniel H Huson March 18 2009 MetaSim Daniel H Huson and Felix Ott with contributions from R Schmid A F Auch and D C Richter www ab informatik uni tuebingen de software metasim Contents Contents 1 Introduction 2 Getting Started 3 Obtaining and Installing the Program 4 Program Overview 4 1 General concept of MetaSim 2 20 020 a 5 Main Window Bo Project Iree Panel ao nea bie dos a aeea Heo ao nee ee ee a ae ed Me Mani Panel o 2 44544 44400 BRYN E ob ee EER Ew ERE ee RE ed pc Mesage Panel css 44 eee ke ee Re Pea Oe ee ee a UR 54 File Ment os cs 2444082804 86 2 bbe es be EAS eb EN ee BE eo ee pe PERA VR do kg ue Ae ee ee CRC RREO a ee ek a ew E E 5 6 Database Menu 5 7 Project Menu 5 8 Window Menu 5 9 MetaSim Menu BLO Tool Bare aaa mma m 6 Database Functionality 6 1 Importing Sequence Files 6 2 Structure usas 6 3 Searching the Database 6 4 Exporting Sequence Files 7 Taxon Profiles 7 1 Creating Profile Files 7 2 Editing Profile Files 7 3 Profile File Format 7 4 Split Abundance Value 8 Simulation Parameter Settings 8 1 454 Parameter Settings 2 2 2 0 5 42 sa eR Re Re wee 8 2 Sanger Parameter Settings 2 ee ee 8 3 Empirical Error Model Parameter Settings 22 02 0004 8 4 Exact Model Parameter Settings
17. View Hide Node Labels 24 View Show Edge Labels 25 View Show Node Labels 24 View Sparse Labels 25 View Use Magnifier 24 25 View Zoom to Fit 24 25 Views 24 Whole Words Only 20 Window About 11 Window How to cite 11 Windows 5 6 X 19 x 1 29 x 2 29 Y 19 Yule Harding 21 Zoom to Fit 24 25 34
18. cted then only strings matching the complete query string will be returned e Ifthe Case Sensitive item is selected then the case of letters is distinguished in com parisons e Ifthe Regular Expression item is selected then the query is interpreted as a Java regular expression e Ifthe Forward item is selected the search proceeds in forward direction e Ifthe Backward item is selected the search proceeds in backward direction 20 e Ifthe Global item is selected the search scope comprises all contained text e Ifthe forward item is selected the search scope comprises only the selected text Press the Close First or Next buttons to close the dialog or find the first or next occurrence of the query respectively Press the Find A11 button to find all occurrences of the query 11 Population Sampler MetaSim includes a Population Sampler that optionally generates a set of evolved mutated offsprings derived from single source genomes using a given evolutionary tree This tree describes how the offspring sequences descend from the source sequence By default a random pyholgenetic tree is generated under the Yule Harding model 3 1 but alternatively user defined trees can also be loaded As asimple model of DNA evolution the Jukes Cantor formula is applied to estimate a probability of change for each base pair with a customizable transition rate a 0 001 by default and time t based on the edge weights MetaSim then gen
19. dit gt Find Again finds the next occurrence of a search string Edit Format can be used to format selected tree items e g size color of nodes width of edges etc 12 5 Select Menu Taxonomy Editor The Select menu contains items for selecting different sets of substructures of the tree e The e The e The e The Select Select All item is used to select all nodes edges and labels Select Select Nodes item is used to select all nodes Select Select Edges item is used to select all edges Select Deselect All item is used to deselect all nodes edges and labels that are currently selected 23 12 6 The 12 7 The 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 gt Select Leaves item is used to select all leaves with their labels The Select gt Select Subtree item is used to select a subtree of a selected inner node 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 Taxonomy Editor Options menu contains items for un collapsing nodes and subtrees The Options Collapse item enables to collapse a subtree at a selected specified node The Options Uncollapse item is us
20. e with the resulting reads is displayed With a left click on this item the first fasta entries are shown in the Main panel Main Panel Main Panel displays information of items that have bee selected by the user in the project Message Panel The program writes all messages to the Message Panel 5 4 The 5 5 The File Menu File menu contains the following file related items The File New Project item creates a new project It is displayed in the project tree The File Open item provides an Open File dialog to open a MetaSim project msim The File Recent Projects item can be used to re open a recently opened project The File Revert item can be used to revert an opened project to the saved version This is useful if one wants to undo changes that have been made to the project e g parameter settings The File Save item can be used to quick save the current project The File Save As item can be used to save the current project assigning a name and location The File Print item is used to print the content of the Main Panel The File Close item is used to close a window The File Quit item quits the program Under MacOS this item is contained in the MetaSim menu Edit Menu Edit menu contains the usual edit related items The Edit gt Cut item is used to cut text e g when editing a taxon profile 5 6 The The Edit Copy item is used to copy text The Edit Paste item is used to paste
21. ean Mean length of clone For Sanger sequencing this length defines the mate pairs length Second Parameter standard deviation of clone length Error Model Configuration Expected Read Length Read sequence length in bp This value depends on affects the number of Flow Cycles Number of Flow Cycles This value depends on affects the read length Mate Pair Probability Value betw O and 1 O means no mate pair Mate Pair Read Length Determines the length of both reads of a mate pair Remove Linker Sequence From Output Originally 454 mate pairs include a 44bp linker sequence If checked MetaSim writes both mates reads separately in the output file without any linker sequence If unchecked the linker sequence will be written to the fasta file as well In the latter case a mate pair is written into a single fasta entry Mean Negative Flow Signal A negative flow is a flow of nucleotides in which the sequence to synthesize is not elongated Light intensities of negative flows follow a lognormal distribution N u k u The default value u 0 23 is taken from 2 Std Deviation for Negative Flow Signals The default value k 0 15 is taken from 2 Signal Std Deviation Multiplier The default value 0 15 is taken from 2 Scale Standard Deviation with Square Root of Mean If checked the standard deviation of the light intensity emitted grows with square root of u i e N u k VE Generate Signal Trace If checked the
22. ed to uncollapse expand the whole tree The Options Uncollapse Subtree item is used to uncollapse expand a selected collapsed subtree The Options Collapse Complement item is used to collapse all subtrees except the currently selected part of the tree The Options Collapse at Level item is used to collapse all subtrees at the specified level from the root The Options Set Number of Genomes can be used to set the abundance value copy number of a specific node see Section 12 2 View Menu Taxonomy Editor Views menu contains items for scaling the tree using the magnifier and showing hiding labels The View Zoom to Fit item is used to scale the tree to fit the window The View Fully Contract item is used to contract the tree The View Fully Expand item is used to expand the whole tree The View Use Magnifier item is used to turn the magnifier functionality on and off 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 24 e The View Show Edge Labels item is used to make edge labels visible e The View Hide Edge Labels item is used to hide edge labels e The View Sparse Labels item instructs the program to show only a subset of the taxon labels thus avoiding overlapping labels 12 8 Toolbar Taxonomy Editor For easier access of frequently used functions a Toolbar is provided with the following functions e F
23. equences of a single profile are visible in an induced taxonomical tree based on the NCBI taxonomy see Section 12 The third compound the configuration of Simulation Parameter Settings is independant of the configuration of taxon profiles Each project comes up with four installed presets sequencing error models at startup 454 Sanger Empirical and Exact see Section 8 Each preset defines several simulation parameter such as type of sequencing technology length of reads mate pair probability etc Of course all parameter values are adaptable and new presets can be created easily Each project has its own set of simulation presets but one is able to export and import selected parameter settings More on simulation parameters can be found in Section 8 MetaSim projects can be saved as msim file using the File Save As item Parameter settings and taxon profiles of all projects are recovered upon startup of the program 5 Main Window The Main Window comprises of three different panels a Project Tree a Main Panel and a Message Panel 5 1 Project Tree Panel This panel displays the database and all existing projects hierarchically in a data tree The first root node represents the Database Clicking on this node will open the database view in the main panel If sequences are already loaded into the database they are listed in the database table If projects have been already created they are listed below the database item Each pro
24. erates the designated number of evolved genomes and then adds them to the internal genome database 11 1 Usage of Population Sampler To generate a set of offsprings for a single genome sequence select a sequence in the database and use Database Evolve Selected Sequences The population sampler window will appear with the following parameter settings e Tree File The user can import his own tree file The Yule Harding tree is loaded by default e Number of Leaves Determines the number of leaves amount of desired offspring sequences e Jukes Cantor Model Alpha Transition rate a default 0 001 After clicking on the Evolve Button MetaSim generates the desired number of new mutated genome sequences Offsprings These offsprings are added to the database directly following the source sequence entry To export the generated offspring sequences one can use Database Export Selected Sequences 11 2 Naming Convention Offspring sequences have the following naming convention The name of their original sequences their name is taken and automatically extended with two additional tags an ascending offspring id and an artificial taxid 21 For example if Acaryochloris marina MBIC11017 is the source genome and the user decides to generate 100 offsprings the final offspring sequence names in the database look like this Acaryochloris marina MBIC11017 OFF_0001 taxon0006 Acaryochloris marina MBIC11017 OFF_0002 taxon0003
25. h preset determines a couple of parameters like type of sequencing technology mate pair probability error probability read length etc The current settings of each preset error model are displayed in the main panel by clicking on a simulation preset in the Project Tree Existing presets can be individually adapted and additional presets can be easily created by using Project Create New Preset To edit an existing preset select a preset in the project tree and use Project Edit Selected Preset To interchange simulation settings between different projects use Project Export Selected Preset and Project Import Presets By default MetaSim contains four different presets representing different sequencing approaches In the following for each preset all parameters are described that can be adapted in the preset configuration window It can be opened using Project Edit Selected Preset 8 1 454 Parameter Settings To simulate read sequences generated by the pyrosequencing approach Roche s 454 e Primary Configuration Preset Name Title of preset Number of Reads or Mate Pairs Number of read sequences to generate x mate pairs means 2x reads Error Model 454 Empirical Sanger Exact 15 8 2 DNA Clone Size Distribution Type Uniform Normal A Clone in MetaSim is a DNA fragment that is randomly extracted from the source genome sequence for read mate pair sampling Selection how the length of the clone is distributed M
26. ile Print e 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 view horizontally button shrinks the tree horizontally e View Zoom to Fit e View Fully Contract e View Fully Expand e View Use Magnifier e Fdit Find 13 Command Line Options As an alternative to the graphical user interface MetaSim can be controlled via command line mode Therefore naviagate to the MetaSim installation folder and execute MetaSim cmd lt option s The MetaSim program is controlled by options Here we list all available options Use the h option to obtain a listing of all options command line options directly from the program Here is an example MetaSim cmd mg usr local metasim examples errormodel mconf r10000 usr local metasim examples example profilel mprf The previous example means start MetaSim in command line mode Use the empirical error model with a specified error model config file Generate 10000 reads and use the specified taxon profile alternatively provide a fasta file with a single genome sequence Then MetaSim uses only this genome to sample the reads from 25 r f t v W 4 reads VALUE Sets the number of reads or mate pairs to generate clones mean VALUE Sets the mean
27. irectory of the installation directory The precise location of the installation directory depends upon your operating system e illumina error model mconf This file contains the empirical error model for the Ilumina Sequencing Technology for a read length of 36bp It can be loaded if the Empirical Error Model is chosen as simulation preset e example taxon profilei mprf This is a really simple taxon profile It contains only four entries demonstrating the structure of a typical taxon profile 29 e example taxon profile2 mprf A taxon profile containing 11 diverse taxa from many different phylae e example project 1 msim An example project Note To be able to generate reads with these example profiles the user first has to fill the database with the appropriate genome sequences Our recommendation is to download the file with all available genome sequences from the NCBI homepage see Section 6 1 References 1 E F Harding The probabilities of rooted tree shapes generated by random bifurcation Ad vances in Applied Probability 3 1 44 77 1971 2 M Margulies M Egholm W E Altman S Attiya J S Bader L A Bemben J Berka M S Braverman Y J Chen Z Chen S B Dewell L D J M Fierro X V Gomes B C Godwin W He S Helgesen C H Ho G P Irzyk S C Jando M L I Alenquer T P Jarvie K B Jirage J B Kim J R Knight J R Lanza J H Leamon S M Lefkowitz M Lei J Li K L Lohman H Lu V
28. is added to the Taxon Profile folder in the Project Tree By clicking on the taxon profile its contents are displayed in the Main Panel To start a simulation use Project Run Simulation to open the final configuration window First select one of the available simulation setting presets The presets can be of course individu ally adapted refer to Section 8 Second choose the desired taxon profile by un ticking the boxes for the listed profiles Finally click on the button Run Simulation to start the simulation After each simulation process a new subfolder yellow colored is added to the project folder containing a log file and a snapshot of the compressed multifasta file with the simulated reads The multifasta file is written into the folder where the project has been saved to 3 Obtaining and Installing the Program MetaSim is written in Java and requires a Java runtime environment version 1 5 or newer freely available from www java org MetaSim is installed using an installer program that is freely available from www ab informatik uni tuebingen de software metasim There are four different installers targeting different operating systems e MetaSim windows 0 9 5 exe provides an installer for Windows e MetaSim macos 0 9 5 sit provides an installer for MacOS e MetaSim linux 0 9 5 rpm provides a RPM package for Linux e MetaSim_unix_0 9 5 sh provides a shell installer for Linux MacOS and Unix The executable program
29. is called MetaSim The unix and linux installers additionally provide an executable called MetaSim cmdline 4 Program Overview In this section we give an overview of the main design goals and features of this program Basic knowledge of the underlying design of the program should make it easier to use the program MetaSim is written in the programming language Java The advantages of this is that we can provide versions that run under the Linux MacOS Windows and Unix operating systems A potential draw back is that an algorithm implemented in Java will generally run slower than the same algorithm implemented in C or C The program is designed to be run in GUI mode A Message Panel provides information about the progress of the program Additionally MetaSim can be controlled from the command line by typing MetaSim cmd and using switches such as r 5000 to set all aspects of a simulation Known genome sequences fasta files are the input for MetaSim These source sequence are internally stored in a database The user then specifies the taxa composition and abundances in a profile file or via a tree editor in GUI mode The sampling of the reads is based on the chosen sequencing technology and error model Output is a collection of reads in a multifasta file optionally compressed The fasta header of each read contains multiple information e the source genome e the sampled position of the reads in the source genome and e the base p
30. is the possibility to assign abundance values not only at the species level but also at higher taxonomical levels The overall abundance value is shared by an arbitrary number of sequences listed below The syntax is lt shared abundance value gt lt gt note the lt gt lt key identifier gt lt key value gt note the at the beginning of the line lt gt lt key identifier gt lt key value gt lt gt lt key identifier gt lt key value gt 14 Here is an simplified example The overall abundance value of 30 shall be uniformely assigned to two genome sequences say MetaSim taxon profile 30 split into 15 Escherichia coli str K12 substr W3110 15 Pseudomonas aeruginosa PA7 HHH 30 taxid 316407 taxid 381754 The amount of 30 genome copies is split and uniformly applied to two genome sequences identified by their taxonomic ids Escherichia coli str K12 substr W3110 and Pseudomonas aeruginosa PAY Likewise both taxa are assigned an abundance value of 15 This feature of a split abundance value is especially needed for the Taxonomy Editor There one can assign abundance values to an inner node of the taxonomy e g Shewanella at genus level to get an uniform mixture of all species in the subtree of Shewanella 8 Simulation Parameter Settings A preset is a configuration of simulation parameters for the generation of read sequences MetaSim already provides four in built presets Eac
31. ject folder has several subfolders e Simulator Settings This subfolder originally contains four simulation presets 454 Empiri cal Sanger Exact Presets determine the simulation settings for simulation runs sequencing technology parameters See Section 8 and can be individually adapted Further presets can be added by right clicking on the Simulator Settings node and choosing Create New Preset This is further explained in Section 8 By clicking on a preset in the project tree an overview of the settings will be displayed in the Main panel e Taxon Profiles In this folder each taxon profile is listed that has been previously created By clicking on a profile item the Main panel displays the content of the profile file By right clicking on the Taxon Profiles node and choosing New Taxon Profile anew profile file will be created All existing profile files can be edited within MetaSim by clicking on the Text Editor Button at the bottom of the Main panel Changes are written to the file when the Done button is clicked More on Taxon Profile can be found in Section 7 5 2 The tree 5 3 simulation run folder After each simulation run a result folder is created named with the current date and time Within this folder a simulation log can be found which contains information on the type of simulation its parameters and the generated output number of reads created etc Additionally a snapshot of the generated multifasta fil
32. ll fasta headers contain multiple information separated by r lt nr of read gt lt indexr gt SOURCES GI lt gi number gt lt backward bw or forward fw read gt lt sample position gt ERRORS lt list of generated base errors gt SOURCE_1 lt name of genome gt lt MetaSim s hash key of source sequence in database gt Here is an example split into several lines for better overview gt r30 1 SOURCES G1 49474831 bw 494076 494112 ERRORS 33 G 40_1 C 43_2 G 53 SOURCE_1 Bartonella henselae str Houston 1 6044c4ffa5bc1b2f851929708279679ab66dcc19 The list of inserted errors contains a single comma separated entry for every error The base positions refer to the sampled and unmodified read sequence The symbol _ represents insertions the symbol represents deletions The remaining entries are substitutions Referring to the mentioned example read r30 1 has been sampled from the B henselae str Houston 1 strain with gi number 49474831 from the base positions 494076 494112 It has been sampled as a single backward read mate pairs consist of two indeces x 1 and x 2 The read has been modified At position 30 the base has been substituted with a G At position 40 one C has been added At position 43 two G have been added The base at position 53 has been deleted 15 Examples Example files are provided with the program They are contained in the examples sub d
33. m A Sequencing Sim ulator for Genomics and Metagenomics 2008 PLoS ONE accepted The research field of Metagenomics is based on the isolation and characterization of DNA from environmental samples without the need for prior cultivation of microorganisms In contrast to single genome studies analyses are applied to entire communities of microbes instead of only few isolated organisms It has already led to exciting insights into the ecology of different habitats The research field of Metagenomics is spurred by the recent development and improvement of next generation sequencing technologies like Roches 454 pyrosequencing Although these high through put technologies promise faster and relatively inexpensive generation of reads Sanger sequencing still has been used in environmental genome projects to avoid the drawbacks of shorter read lengths The aim of MetaSim is to provide a tool for the simulation of reads based on given genome sequences reflecting adaptable error models of current sequencing technologies Additionally the user is able to determine the abundance of the chosen taxa Therefore MetaSim integrates an induced tree view of the NCBI taxonomy that can be used to interactively select taxa and inner nodes of the taxonomy to configure their relative abundances Another feature of MetaSim allows the user to simulate an evolved population of a single genome sequence using a population simulator This feature is aimed at simulating
34. n Rate can be defined lt preceding base gt lt from gt lt to gt lt value gt marks optional parameters Set switch rates for A following G G A T 0 4 G A C 0 3 G A G 0 3 Alternatively set switch rates for all C C T 0 3 C A 0 3 C G 0 4 Further the Empirical Error Rates can be defined in the same file The specification of error curves is done by listing the probability values row wise per base position E g for a 35bp read 35 probability values have to listed The header of such a list must contain one type of error SUBSTITUTION_ERROR INSERTION_ERROR or DELETION_ERROR In that case all bases A T G C receive equal error rates For example lt error type gt Set all substitution rates SUBSTITUTION_ERROR 0 00606508512067950 first base 0 00675296642376962 0 05190994307855664 last base If one wishes to assign error rates to a specific base one can use lt error type gt lt base gt marks optional parameters Set insertion rates for every A INSERTION_ERROR A 0 00606508512067950 first base 0 00675296642376962 18 0 05190994307855664 last base Additonally one can define error rates for a specific base that is preceeded by another base For example lt error type gt lt preceding base gt lt base gt marks optional parameters Set substitutions rates for a G following an A SUBSTITUTION_ERROR A G 0 00606508512067
35. n of a metagenome dataset that represents the set of source genome sequences for read sampling In a text based profile file each row lists one genome sequence together with its desired abundance value 7 1 Creating Profile Files Profile files have the file ending mprf and can be created and edited with any text editor Alter natively taxon profiles can be created within MetaSim by right clicking on selected entries in the database and using Database gt Create Taxon Profile from Selection 7 2 Editing Profile Files Editing can be done with any text editor or the in built Text Editor of MetaSim can be used To display the text editor in the main panel select a taxon profile in the Project Tree and click on the Text Editor button at the bottom right of the main panel All changes will be written to the file if one clicks on the Done button In case the file format see Section 7 3 is incorrect or if the program is not able to find the mentioned genome sequences in the dabase the icon of the taxon profile in the Project Tree shows a Red Exclamation Mark Otherwise a green colored check indicates that the taxon profile is valid If a taxon profile has been edited with an external text editor MetaSim has to update the file content For this right click on the concerned taxon profile and choose Reload Selected Profile 13 7 3 Profile File Format Each line in a taxon profile represents a single genome sequence and has the following s
36. ond parameter std max deviation of the sanger read length distribution Sanger uniform Use a uniform read length distribution for sanger reads sanger err start VALUE Sets the initial error rate for the sanger error model sanger err end VALUE Sets the final error rate for the sanger error model sanger deletions VALUE Sets the relative deletion rate for the sanger error model sanger insertions VALUE Sets the relative insertion rate for the sanger error model sanger mate probability VALUE Sets the probability of paired reads Sanger error model m empirical Apply the empirical solexa error model to the generated reads g empirical cfg VALUE Specify an empirical error model config file 2 empirical read2 cfg VALUE Specify an empirical error model config file for the 2nd read empirical pe probability VALUE Specify paired end probability for the empirical error model 27 empirical readi mi empirical read2 mi a add files add archives test db description VALUE length VALUE taxupdate VALUE X print taxids c combine uniform weights threads VALUE Z compress q no progress seed VALUE d output dir VALUE s simple output name h help 14 File Formats d2end read 1 ends at insert end for the empirical error model d2end read 2 ends at insert end for the empirical error model Add the provided fastA file
37. ositions where the read sequence was modified by the selected error model 4 1 General concept of MetaSim The aim of MetaSim is to provide a flexible tool that enables the user to design several simulation runs with e g 1 the same sequencing technology but with different genome sequences 2 the same sequencing technology but with different x fold coverages 3 the same genome sequences but with different sequencing technologies 4 the same genome sequences but with different abundance values 5 etc For this the overall organisation of MetaSim is based on three compounds a database holding the genome sequences taxon profiles and simulation parameter settings The Database provides all genome sequences the user previously has to import see Section 6 Only those names of genome sequences present in the database can be listed in Taxon Profiles to determine which genomes should be taken as source sequences for the simulation of reads In this way the composition of metagenomes can individually be determined See Section 7 1 to see how a taxon profile is structured A single project can contain several taxon profiles Prior to simulation of a project one is able to select the desired taxon profile s If the genome sequences in the database are assigned a unique taxonomy id taxid see Section 6 1 how to import this information the text based taxon profile can be visualized in a Taxonomy Editor In this window all taxa genome s
38. resents a collection of genome sequences that are available for the read sampling The database is based on the HSQL database engine http hsqldb org 11 6 1 Importing Sequence Files To start working with the program you must first import one or more databases of genomes Use Database Show Database to activate the database 1 You can use your own multi fasta files or simply download all prokaryotic sequences from ftp ftp ncbi nlm nih gov genomes Bacteria all fna tar gz 738MB Import your gzip com pressed files using Database Import Files 2 To additionally work with virus sequences in the same way download and install ftp ftp ncbi nih gov refseg release viral virall genomic fna gz 3 For the program to function correctly please also download the file ftp ftp ncbi nlm nih gov pub taxonomy gi taxid nucl dmp gz 345Mb and then pro vide it to MetaSim using Database Get Taxon IDs by GI Alternatively use the menu item Database Get Taxon IDs NCBI ftp to download and parse this file in one step This may take some time Importing the genome files has only to be done once Imported sequences are kept in the database even after closing the program so they are still available when you restart MetaSim By default the database is placed in the installation folder of MetaSim You can change the location using Edit Preferences Set Database Location 6 2 Structure To see the content of the database
39. s The Exact Error Model is suitable for sampling reads without modifying any bases i e in contrast to the other provided error models no substitution insertion or deletion will be applied to the read sequences e Primary Configuration see Primary Configuration of 454 preset e Simulator Options see Simulator Options of 454 preset 9 Run Simulation Window The Run Simulation Window opens if the user clicks on the Run Simulation button or by using Project Run Simulation Before a simulation run the user has to configure which simulation settings and which taxon profiles should be used The settings can be chosen from the pull down menu Additionally all marked taxon profiles are used for the simulation Note that it depends on the setting Merge All Files Into a Single Taxon Profile whether the reads of all marked taxon profiles are merged together into one multifasta file or not If the simulation has been successful a new result folder is created within the Project Tree 10 Find Window The Find Window can be opened using the Edit Find item Its purpose is to find sequence entries in the internal database or any text in the simulator settings taxon profiles and the message panel Depending on the current view in the Main Panel the user can select from different targets in the Find window A target is a panel that can be searched Use the following check boxes to parametrize the search e Ifthe Whole Words Only item is sele
40. s to the database Add fastA files from tar gz archives to the database Test the database integrity Print out the description of sequences where the hash string starts with VALUE Print out the length of sequences where the hash string starts with VALUE Update taxon ids from a sorted and gzip ed gi to taxon id map file print a sorted list of all taxon ids present in the database Combine all files to a single simulation Do not weight sequences by size and number of per genome copies Set number of readsim threads 0 runs in serial mode default 1 Compress output Suppress all progress information Sets the random seed To obtain reproducible results threading must also be disabled Specify the output directory Don t hash time stamp in name of output file Display this help and exit MetaSim uses and produces three file formats e msim This is the main Project File about a project such as simulation presets contained taxon profiles and log files e mprf Files having such an ending are Taxon Profile files It determines the composition and abundance of selected taxa 28 XML format that saves all necessary information e mconf These files are used to define individual Empirical Error Models 14 1 FASTA header of Output Files Output of MetaSim are multifasta files with the generated read sequences To be able to trace back a read source genome sampling position insertion of errors a
41. tructure lt abundance value gt lt key identifier gt lt key value gt 1 abundance value is a relative number of arbitrary size reflecting the copy number of the genome sequences of this specific taxon in the total taxon set 2 key identifier corresponds to the column names of the database suitable to identify a genome sequence This can be taxid gi or name When using the name identifier one is able to use as wildcard symbol as it is used as wildcard symbol in SQL syntax 3 key value the corresponding value the for chosen key identifier A line starting with is treated as comment and is ignored Here is an example for a taxon profile MetaSim taxon profile 100 Methanoculleus marisnigri JR1 50 Alcanivorax borkumensis SK1 HHH 100 name Methanoculleus marisnigri JR1 50 name Alcanivorax bork A number of 100 genome copies abundance of Methanoculleus marisnigri JR1 and 50 genome copies of Alcanivorar borkumensis SK1 are part of this meta genome dataset If the wildcard symbol is used for a name and the database contains multiple sequences having the same prefix the abundance value is assigned to every genome sequence For example if a line is like 50 name Escherichia coli all available E coli strains together with their plasmids are added to the profile with the same abundance value 100 7 4 Split Abundance Value A special feature of the program
42. uences from each other The Database Set SQL Query item can be used to query the database with the standard query syntax See Section 6 3 The Database Reset SQL Query item resets the SQL query to SELECT enabled gi taxid name circular copies length FROM sequences ORDER BY name Project Menu Project menu contains the usual project related items The Project gt Add Files item is used to import further genome sequence files such as multi fasta files The Project Remove Selected Files can be used to remove selected files from a project such as simulation presets taxon profiles or output folders The Project New Taxon Profile item opens a file dialogue enabling to create a new file A new empty taxon profile will then be added to the Taxon Profile folder of the Project Tree It can be edited by any system text editor or the in built editor of MetaSim see Section Rea The Project Reload Selected Profile item reloads a taxon profile in case it has been changed with an external text editor The Project Rename Project can be used to rename the project string The Project Create New Preset item opens the simulation settings window After adjusting all parameters a new preset is added to the Project Tree 10 5 8 5 9 The Project Edit Selected Preset opens the simulation settings window for a selected preset The Project Import Presets item imports a file mprs defining a simulation setting preset
43. value of the fragment lengths clones param2 VALUE Sets the second parameter std max deviation of the fragment length distribution uniform clones Use a uniform fragment length distribution instead of gaussian empirical clones VALUE 454 454 454 454 454 454 454 454 454 454 Use a two column file with empirical insert size counts to generate the fragment lengths instead of gaussian Apply the 454 error model to the generated reads cycles VALUE Sets the number of cycles 454 error model mate probability VALUE Sets the probability of paired reads 454 error model paired read length VALUE Sets the read length for paired reads 454 error model remove linker remove linker sequence from paired reads 454 error model nosqrt Signal distributions stddev k mean instead of stddev k sqrt mean 454 error model multiplier VALUE Sets the proportionality constant for computation of signal std deviations 454 error model logn mean VALUE Sets the mean of the lognormal negative flow signal distribution 454 error model logn std VALUE Sets the std deviation of the lognormal negative flow signal distribution 454 error model trace Use an explicit signal trace 454 error model 26 sanger Apply the sanger error model to the generated reads sanger mean VALUE Sets the mean value for sanger read lengths sanger param2 VALUE Sets the sec
44. ving the profile in the Project Tree is updated 12 2 Setting the Number of Genomes By using Options Set Number of Genomes the user can determine the abundance value of a specific node or leaf of the taxonomy tree Can also be done by right clicking on a node This 22 number equals the value defined in the text based taxonomy profile for each genome sequence The higher this value the bigger the node leaf is displayed in the tree A useful feature is to assign such a value to an inner node instead to a leaf specific genome sequence of the taxonomy Section 7 4 explains this in more detail 12 3 File Menu Taxonomy Editor e The e The e The file e The e g e The e The e The File Open Taxonomy Editor item opens an existing taxon profile mprf File Save Taxonomy Profile item quick saves the current taxon profile File Save Taxonomy Profile As item saves the current taxon profile to a mprf File Export Image item can be used to export the current view to a graphics file eps gif jpg png svg bmp pdf File Print item is used to print the current view File Close item is used to close the taxonomy window without quitting MetaSim File Quit item quits the MetaSim Under MacOS this item is contained in the MetaSim menu 12 4 Edit Menu Taxonomy Editor The Edit Copy item is used to copy text e g nodes labels e The Edit Find item opens the Find Window e The The E
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