mPed User Manual
Contents
1. STRIPPING NO STUD_ID_COL 2 SIRE_ID_COL 17 DAM_ID_COL 18 SEX_COL 4 BDATE_COL 11 Must be a full date if only year is known see below DEATHDATE_col 0 Must be a full date if only year is known see below DEAD_COL 0 T F True or False LOCATION_ID_COL 0 Location name of the place where the animal is kept LOCAL_ID_COL 2 LocallD ID at the place where the animal is kept OTHER_ID_COL 0 OtherID could be used for other IDs or other information about the animal PMx needs a full birth date for each individual If only year of birth is known a full birth date must be created Provide the year of birth and death in columns entitled BDATEYYYY_COL 0 If only the year and not the date of birth is known DEATHDATEYYYY_COL 0 If only the year and not the date of death is known Provide a dummy date for birth and a dummy date for death BIRTHDAY_MMDD 0 DEATHDAY_MMDD 0 Here the parameter value for sex is provided Provide information on how you denote the sexes format_indata SEX_SIRE H SEX_DAM T SEX_UNK U MIN_MAX_BIRTHDAY If you want to make sure you spot erroneous birthdates and ages provide the earliest possible date and or the latest possible date that an individual within the pedigree can have been born Oldest parent provide the maximum age possible for a parent Only Swedish Dog Alive YES or NO is a special parameter for data from the Swedish kennel club stating to only include2. dogs registered in Sweden i e registration number starting with S or SE MIN_BIRTHDAY 1 9000101 MAX_BIRTHDAY 202 11231 10 OLDEST_PARENT 14 ONLY_SWEDISH_DOGS_ALIVE NO SIMULATED_DEATH_DATE Birthday to death if information on death date is missing in your pedigree you can provide a maximum age after which all individuals die Make birthday for individuals that lack birth dates and birth years and are parents you can make dummy birthdate by providing information on the age integers of parents at first time of reproduction Example 2 parents are born two years prior to their first offspring 0 donot create dummy birthdates LONGEVITY 12 MAKE_BIRTHDAY 2 COMMENTS Comment_in_output If YES information about the ini file is provided in the ped file File suffix optional if you want you can add an extension maximum eight characters to your file name e g pedigree_10 ped where _10 is the extension Local_ID amp Other_ID set these parameters to a set same for all individual optional value data_default COMMENT_IN_OUTPUT YES FILE_SUFFIX ij LOCAL_ID optiona OTHER_ID optiona 11
3. following order 1 Analysis date 2 Stripping 3 Excluding individuals with blank birth date Acknowledgement Thanks to Mari Edman for help with usability testing of mPed and proofreading of this manual The ini file with user input marked in yellow INITIALIZATION FILE for mPed version 1 2 This file provides instructions for mPed about the organization of the pedigree input file Please change the information below as required for your analysis Analysis date individuals born after this date are not included in the ped file Include blank birthday If YES individuals lacking birth date will be included in the pedigree and considered as dead If No such individuals will be removed from the pedigree Stripping If YES removes individuals who are dead and lack descendants among living animals If NO all individuals are included in the generated ped file _col informs mPed in what columns information about the separate individuals can be found Exampel STUD_ID_col 2 the id of separate individuals is located in column number 2 of the input file The _col parameters are denoted as in PMx please see manual for details Date fields must be formatted as yyyymmdd e g 20110315 yyyy mm dd or mm dd yyyy e g 3 15 2011 One or more files could be read simultaneously INPUT ANALYSIS_DATE 20101009 FILES c mija h txt INCLUDE_BLANK_BIRTHDAY YES
4. use to record further information about each animal but these additional fields are not supported in mPed GETTING STARTED System Requirements mPed requires e RAM 256 MB or more e OS Windows 7 Windows Vista or Windows XP must have SP3 32 or 64 bits Installation The mPed installation package can be downloaded from www popgen su se mped php This installation package should be saved in the local computer where it can be run 1 For Vortex 1 female 0 male The input file The input file should be a tab separated text file and you need to transform your studbook data to this format This can easily be done in e g MS Excel by choosing Save as Text tab delimited txt Example of studbook in MS Excel a a testfil xls Read Only Compatibility Mode Microsoft Excel Home Insert Page Layout Formulas Data Review View Add Ins 4 p ginsety E ly 4 Colibri vit Ax I S Wrap Text General EA 7 ee Ba g Delete 3 Paste Biu Oy Ay BBB EE H Mege amp Center 7 v 4g 303 Conditional Format Cell ps X F em ae E E i i id Formatting as Table Styles Format lt 27 i Clipboard Font Alignment Number Styles Cells M6 M fe A B c D E E G H I K 1 This is an example input file to mPed 2 Information in columns 2 7 is the minimum of what is required for mPed to create an ped file for input in PMx 3 Column headings refer to parameters used by PMx see manua
5. NT states how much older than the offspring the parents are allowed to be Dates that do not fit this condition will be removed The format is YYMM 2001 means 20 years and 1 month See function h MIN_MAX_BIRTHDAY in the copy of the ini file below i SIMULATED_DEATH_DATE State for how long an animal is assumed to live for populations were death dates are not included j MAKE_BIRTHDAY The function assumes the age of a parent based on its oldest offspring For example 2 results in parents being 2 years older than their oldest offspring and the birth date is thus a date two years before the oldest offspring k COMMENT_IN_ OUTPUT YES or NO Here you choose if you want comments on the output of mPed including information on settings and number of individuals PMx can handle this kind of comments but the older version of PMx PM2000 cannot I FILE_SUFFIX You might add a suffix of maximum eight characters on your output file Date must be formatted as yyyymmdd e g 20110315 yyyy mm dd or mm dd yyyy e g 3 15 2011 These formats are supported in PMx If you only have a year in your available information you have to make up and state the dates that should be added for PMx in for example Birthday_MMDD 0307 Deathday_MMDD 1008 because PMx demands full birthdays In PMx birth dates should be blank or complete If you use several functions that exclude individuals from the output file they are executed in the
6. User Manual for mPed make Pedigree file Version 1 2 December 2012 Division of Population Genetics Department of Zoology Stockholm University SE 106 91 Stockholm Sweden Developed by Mija Jansson Ingvar Stahl and Linda Laikre Reference M Jansson Stahl L Laikre 2012 mPed a computer program for converting pedigree data to a format used by the PMx software for conservation genetic analysis Manuscript Corresponding author Mija Jansson Telephone 46 8 16 42 37 office Fax 46 8 15 40 41 office E mail mija jansson zoologi su se Table of Contents MmPed Wser Manual cic cick nesecs sacegtecvebesecessledvevestusede susedbes Vel uGenlesteleeeyhtve aiie EEE sendin heel tees 1 OVERVIEW AND PURPOSE maois ionian anent aaia a aaaea aaa aiaa aia aaar aaa aana a aea a aaaea 1 Necessary PMXINDUt sisirin ne ee aaisen nonae Ee EEEE Ea ANE EE E E EEE 2 GETTING STARTED iscesssasicdeseaeizesvecudedesatedscvsnncacdedatedtessebadedtonusdeetsensedantegniecsseandeusaadeacevsansicds ade Eaa aaaea 2 System Reg iIremMENtS a2 osc2h lt cocbavieasterecesezebeseasCoscebscdibacewisegsststaebaseee lt osends lt debayenstepecessdebeueenSesacbs lt dibacesisessce s 2 eE eE E E A 2 THE AMP UC HIS sasoiean eeaeee eee EEEE EErEE Eee a aea e AEE SE AEON EEEE EEES E NEEESE ERE 3 RUN ta ROG otee e E E a E E E e e E vtec 3 Output TIES THOM MPC sredite a acesteveess de d daccaeenedeasseegatsadosaeesdeanderess casgenancesert sh csadesiedeteescedeeesd 4 T
7. dered as dead If No such individuals will be removed from the pedigree Stripping If YES removes individuals who are dead and lack decendants aon living animals If No all individuals are included in the generated ped file _col informs mPed in what columns information about the separate individuals can be found Exampel STUD_ID_col 2 the id of separate individuals is located in column number 2 of the input file The _col parameters are denoted as in PMx please see manual for details Date fields must be formatted as yyyymmdd e g 20110315 yyyy mm dd or mm dd yyyy e g 3 15 2011 One or more files could be read simultaneously Soba Analys_date 20120103 Files t txt Include_blank_birthday YES Str ipping No STUD_ID_col 2 BDATE_col 5 Must be a full date if only year is known see below lt Explaining text marked with semicolon is automatically excluded when the program is executed Instructions to define the input file with pedini ini a Open pedini ini b The pedini ini starts with stating the analysis date for example 19951231 All individuals born after that date will be excluded from the file If all animals are to be included state today s date c State path to the input file If you want to run several files at once you can state an asterisk in the file name see example below Files D Mija _hundarMaj h2011feb_ORIGINAL h txt In this case every
8. file that starts with an h in the folder will be analyzed d If you want to include individuals that lack birth date in the analysis type YES to include blank birth date otherwise type NO to exclude individuals that lack birth date If you have animals that lack birth dates but that you know are alive we recommend that you first run the file through mPed and then manually change the dead T F column e mPed can remove unnecessary parts of the pedigree i e lineages which are extinct because the ancestors do not have any living decendants to make it easier to run PMx Such removal of individuals is called stripping State YES or NO in the ini file depending on if you want to strip off unnecessary individuals or not f Define from which column the column number in the input file the information data should be collected E g STUD_ID_col 2 means that your ID for each animal are placed in column two If you lack information for a certain column just state O NB If you are going to use ONLY_SWEDISH_DOGS ALIVE set DEAD _col gt 0 even if you leave the fields blank g Define format for the animals sex For example F for female and M for male h MIN _MAX_BIRTHDAY You can choose a latest possible and or an earliest possible birth date of individuals if you want to make sure that erroneous dates in this respect are deleted the individual will lack birthdate OLDEST_PARE
9. hE MPED A Til Essonne aeee enee a iaae AEE oaa EE EEES SEE EE EEEE REEE EAEN aTi 6 Acknowledgement soiirci e a e e a aaa e e aeara e 8 The ini file with user input marked in yell0W ssssssssesnnssssssnsenrnssssssrrernrssssssrrernnsssssserennnssssenrneennssssenne 9 mPed User Manual OVERVIEW AND PURPOSE mPed is a program for converting pedigree data into an input file that can be used by the software PMx PMx Population Management x Ballou J D Lacy R C amp Pollak J P 2011 PMx Software for Demographic and Genetic Analysis and Management of Pedigreed Populations Version 1 0 Chicago Zoological Society Brookfield Illinois http www vortex9 org PMx html is a free software developed for conservation genetic and demographic analyses and management of pedigreed zoo populations PMx was designed to aid the management of populations for which the aim is to maintain the genetic diversity as close as possible to the source population over time PMx was developed as an accessory program to the Single Population Analysis and Records Keeping System SPARKS ISIS 2005 User Manual for SPARKS Version 1 5 ISIS Eagan USA http www2 isis org support SPARKS Pages home aspx software for studbook record keeping SPARKS is the international platform for zoo population studbooks Input files for PMx are created by SPARKS Today more and more populations outside the zoo community are managed to maintain genetic diversity This i
10. l for details 4 Column 2 3 4 5 6 7 8 9 5 Name ID SireIlD DamiD Birthdate Sex Dead Info Adam 1 WILD WILD M E bald first founder 7 Eva 2 WILD WILD F Li punished first founder 8 kim 3 1 2 u T 9 Abel 4 1 2 M T childless 10 Kain 5 1 2 20060101 M F 11 Set 6 1 2 M F 12 Linda 7 UNK UNK F F professor 13 Peter 8 5 7 20100510 M F 14 Lovisa 9 6 7 20111231 F F 35 Mija 10 6 7 F F M 4 gt M Sheet1_Sheet2 Sheet3 2 la Ready UH 10 O o amp 8 a4 c Fz I A Sot amp Find amp Filter Select Editing The same procedure works for other database programs In MS Access for example you choose to export your data base with tab as delimiter If you want to make notes or comments in the input file you just put an asterisk left of the note An is also needed before any headings if you have kept those in your text file RUN mPed To run mPed you have to put your tab separated text files in the same folder as you put the mped exe and pedini ini files see instructions for the ini file below To run mped exe you double click on the file and mPed runs pedini ini is read automatically When finished mPed writes DONE A screenshot of mPed Make ped file to PMx lt u 1 gt Oct 23 2012 gt 2 1 ini C mPed test pedini ini gt Now running CC mPed test mped exe gt Ini C mPed test pedini ini gt gt gt gt gt gt gt gt DONE lt lt lt lt l
11. ncludes domestic breeds and wild animals for which pedigrees are available and the management of these populations would benefit from being able to use PMx Although PMx can be used as a stand alone program it requires preparation of an input file in a specific format ped the PMx input file which is complicated to create outside the SPARKS platform Also importing already existing studbooks into SPARKS is very difficult Therefore we developed the mPed make ped file converter program mPed is written in the programming language C and can transform a studbook to a ped file that could be analyzed in PMx Necessary PMx input The following information is the required minimum by PMx with respect to each animal Abbreviation used by PMx Explanation ID Individual identification SirelD Identification of father sire DamID Identification of mother dam Sex 0 female 1 male Selected Individuals are selected to be included in the analysis Two options are possible T true F false Dead The animal is either dead T true or alive F false Birth Date Provide the date when the animal is born Blank if unknown Death Date Provide the date when the animal died Blank if not dead or not known Location Name of the place where the animal is located Local ID Identification of location Other ID Other ID or individual information that you want to add In PMx you can add any additional fields that you wish to
12. t lt lt Output files from mPed Before the output files are created all your files are located in the same directory amp C mPed test mPed File Edit View Favorites Tools Help Q sx z B 2 Search fy Folders mE S Folder sync Address G C mPed test mPed pedini ini wy Configuration Settings mped exe Other Places D test My D B sh T My C GQ my Details 1 70 MB 7 Den h r datorn mPed generates a pedigree file for PMx ped a pedigree file for Vortex txt and one information file f C mPed test mPed File Edit View Favorites Tools Help Q Back 7 Q E PP Search Folders Ez SI Folder Sync Address O C mPed test mPed testfil txt File and Folder Tasks inp Text Document 1KB J Make a new folder Publish this folder to the 2 pedini ini Web Configuration Settings vortex fe Share this folder SS testfl txt_Mija siped testfil_Mija ped S1PED File PED File Other Places 1KB 1 KB D test testfilMija_info _s1 My Documents _S1File 1KB Shared Documents 4 My Computer My Network Places Details 9 Den har datorn The output pedigree files are located in the same directory as your mped exe ini and txt files the file for Vortex is located in an directory of its own in the main directory The ped file can be run directly by PMx and the vortex file can be used directly by Vortex The Vortex file represents work in progress we are currentl
13. y working on generating an input file to the Vortex computer program Both PMx and Vortex can be downloaded free of charge from http www vortex9 org The information file The first section contains information on the input data e Number of animals born certain years e Number of males females e Number of unknown ancestors The second section of the file contains the same information for the result of running the pedigree through mPed Check your ped file If you want to check your ped file before running it through PMx use for example MS Excel a start MS Excel b choose Open and file c choose Delimited d choose Semicolon The mPED ini file mPed obtains instruction about the structure of the pedigree file the tab delimited txt file and modifications needed from the ini file The ini file is a text file in which the user changes and saves necessary instructions information for mPed A screenshot of the ini file for full text see below DP pedini ini Notepad File Edit Format View Help INITIALIZATION FILE for mPed version 1 1 This file provides instructions for mPed about the organization of the pedigree input file Please change the information below as required for your analysis Analysis date individuals born after this date are not included in the ped file Include blank birthday If yes individuals Jacking birthdate will be included in the pedigree and consi
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