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1. Ok I Cancel Project Folders and Paths Projects in Eval is by default located in the lt path to Eval application gt Projects folder and if you place all your projects in this folder you will be able to move the Eval application to another folder on your computer or to another computer simply by copy the application folder On the other hand if you do not place your projects in the projects folder they will not be available if you move the Eval application they are simply removed from the project catalogue not removed from disk The Default Project The Default project is a project that is automatically created if for any reasons Eval fails to load a project The Default project 1s used whenever Eval fails to load either the last opened project or if a project 1s removed from the disk You may perceive the default project as a starting point for a new project or as a quick way of creating a ftestO project which you later may save as a proper project When not saving the default project as a new project it will become your new default project next time you start Eval This has the possible hazard that Eval can not start because of a corrupted default project A corrupted default project or any project for that matter can occur when the user you force to stop Eval in the middle of a computation If this happens take a look in the Failures and possible solutionsO chapter for a solution Project Catalogue
2. Your compliment use period has ended Thank you for u PDF Complete Interface User Manual VERSITET Software By Peer Berg Morten Kargo S rensen Jes Nielsen Updated 27 02 2009 13 55 00 Your complimentary use period has ended Interface User Manual Thank you for using PDF Complete VERSITET eed Features Index Podne O ee E N EE 3 Minh 4 Inbreeding I reasons and CONSEQUENCES ccecceeeeeseeceeeceeceeees cess cessecueesaeeeceeeceeeceesesessesseesseeeees 4 Balance between genetic gain and additive genetic relationship u u dsssseeneeeeeeereee seeren sene eee 4 Eya EE CO VCE ERE E 5 nl 6 UN 6 EET 5 EE E A E E 6 PUY SENER EE EEE 7 FUNN 8 Recommended installation folder rrrrarrrarnrrnnnnrnnnnvnnennrrnrnnnvarnnnnsr maner nnnevnnennnnnsnnnnarsnnensn eee vene 8 Installed Folders and what they contaln roronnnnnnnnrrrnnvrrnrrrnnerrnnnnernnnennnnn varen nnrnsnnnenernnansn mane vene 8 NTN nctiannacoeaber ERE S EE 9 U CD ROM e sere an secand neteneuctonst ace aeeeqeatoecuserece sonacs wovaeaaueannsdvace smear dscaceeera se 10 Uor EEE EE SE EE 11 RUS ars PRN oe EEE OE T E E E 12 luv b0wins aasebeesnes aaudaencou E A E E 14 Updating the Eva Interface Installation srecne cae a a a 15 E E OOS REE T Eee es adel Eee EGER 16 Data liput to Eva OT Ty ATi ERE ERE 16 Dili 17 PEER GE gt E e E EE EE ae E T 18 FP 19 572 Fede al MCE ERE nose ae aeenn E E E meena 19
3. Your complimentary use period has ended i Thank you for using Com PO e PDF Complete Interface User Manual VERSITET If you proceed the risk of a application crash is extremely eminent Instead of proceeding reduce the number of selected animals and try again To move selected animals back to the available animals list you use the PKO and fk lt Obuttons possible combined with the keyboard keys described above In addition you can order the selected animals by using the two arrow buttons in the right side of the window To move an animal or animals up highlight the animals and then either click the up arrow or the down arrow Please note that in the current version of the Eva Interface after running Eva Inbred the optional text is replaced by the actual animal idG Results from Eva and Eva inbred The result files from the computations in the Eva Interface consist of the output files from Eva and Eva Inbred depending of which program you have used from within the Interface It is possible to view all the computation results and log files in the Eva Interface by selecting the results tab in the bottom of the program panel All results are viewable as text output in a table and most results are also viewable Number of generations als in graphs some are user specified cf Presentation of computation resultsO If further result processing or evaluation is necessary all output files from Eva and Eva Inbre
4. Compress to Menuen Start rar and email Egenskaber Abn mappen Alle brugere Gennemse mappen Alle brugere When your zip program has opened click FAE ESSENS as Resi 1 1 i File Acti Opti Hel the Eval exe file and the installation ee SERD should start o E gy G G w Ee 9 Open Favorites Add Extract View CheckOut Wizard Type Modified Size Program 20 12 2005 19 38 16 042 773 4 b Selected 0 files 0 bytes Total 1 file 15 667KB DW Click the filnstall button to install Eval EZ Installation of Eva Interface 1 3 02 Update L You need a password to install Eval In current version it 1S Magr4sciO but this Please see How to Install on website http eva argsci dk may change in future versions Follow the onscreen guide f Destination folder CA Programmer E va Interface 1 3 02 Browse Installation progress Install Cancel Updating the Eva Interface Installation Note that your projects already on your computer should not get influenced when you update or reinstall Eval but make sure you take a backup of your project files before the update or reinstallation If you use the default project folder then your project are located in the Eval project subfolder Side 15 af 41 Your complimentary use period has ended _ amp Interface User Manual Thank you for using PDF Complete WITKTE EE i ped Features of Eval on a CD ROM or by ema
5. Directed mutation probability 0 Number of generations 10 000 3 Mutation probability i 0 11 E population size 100 E Random number seed ol gt Interval in generations Reset parameter values Warning Do not use Advanced parameters unless you have read and understod the user manual ata file r Parameters f Results Run Eva Project name Default Project path Projects Default Eva inbred Parameters For each animal in the input file Eva inbred calculate inbreeding coefficient generation coefficient and pedigree completeness in a specified number of generations On top of this relationship among animals and the contribution of specific animals to specific groups of animals can be calculated There are three different possibilities to add contribution lines 1 Manually by optional text in the quick add box By animal ids in the quick add box 3 By using the contribution generator which let you select the animals to be included in the computation and then generate all the ancestor descendant combinations automatically Alternatively it is possible to calculate the additive genetic relationship for ancestor animals to another group of animals by inserting an Ancestor in the Ancestor field and then select group from the Ancestor Group drop down box as show below Setting the Ancestor value to 0 zero and the Grou
6. Side 29 af 41 xp ur Features Your complimentary use period has ended C om p let et e Thank you for using PDF Complete 10w every time you start Eval and not having the Eva Interface User Manual VERSITET interface load the last project you i worked on Then do fr interface Project Catalog the following Select the menu project and click on 6 gexenenpojeea Projects Open existing project the menu item Open Last project to remove the Existing project black dot in front of the text Next time you start Eval it will automatically show the project catalogue window from which you can open a previously saved project or create a new project To disable the project catalogue dialog again just click once on the Open Description Last project In the project catalogue you may view the previously saved projects and project descriptions by clicking MOpen existing projectO text and then selecting one of Author Created Path to project Description the projects in the Existing projectsOlist To open a ok cancel Next gt gt gt project just select the project and click the FOKO button Create new project Fields you must provide Author Project name The project catalogue is by default started such that DNL Project Path Description Path to project directory Browse you are able to create a new project immediat
7. Ey Ame Ered 21 Results Tom Eya and B Vase eei EE EE EEEN REEE 23 DEIGEN ne 23 Description of Eva Inbred Rv de A 24 Presentation of computation results ssss seven veee rese seen error enn nnnennnnnnrnnnennsnsnnnessen sansen 26 TN 26 Te 26 Chan KATE iat Tee UG GERE N E 26 nm TN 21 Copying output data to another application rrrornrrrrrrrrrerrrrnrnnnnnnnnnnnnvrnnrnnrrsnnnersrrnannnnnen sunne 28 PO SCE MPAA CCI soc EEE EE ENE eee 28 FN 28 Project Forsand PERS REE EE EEE 29 Me DEPOT 29 Fo TU 29 MOU PAIGE 100 5 e EE EEE E E 30 NET E ERE REE SN 30 SE DE 1 EEE SEE 31 Addins adata Nile 0 your PO eee 31 Running Eva or Eva bred cees A A dendnd d den 32 Running Eva compute breeding scheme ce cccce cess eee events see sees seere senere skeerne ennen e2 Running Eva Inbred computing inbreeding rarrrnnnnnvrrnarrvrnnnrnrnnnvrnnnenernnnnnennnerssrnnnevnnnnesennn 32 PRESSE 33 WAC TRO NE EEE 33 Side 2 af 41 Your complimentary fi use period has ended p interface User Manual Thank you for using PDF Complete IVERSITET aed Features Tips amp tricks cecccsccccsssscccsssssecssssesecssesccssssescssssssessssseccsssssesssssussessseseesssssssssseseessssessessesesssscesssssecsenee 34 Adding Eva and Inbred parameter files to a project arrrrnnnnvrrnnnrrnnnnenrrnerrrennerrrnnnnvrrnnerrrnnnennrseer 34 Fs 35 EKERN EN 36 FOTOS EE EE NE NN 36 Ge RE ENE epededace vase censentee saad obau
8. degree will be related but can also cause problems in large populations which are managed with a very limited number of sires Thus inbreeding presents a challenge both to small conservation populations and large active commercial populations There are however ways to limit the inbreeding problems One of those methods is EVA as presented here By accepting a slight reduction in genetic gain the inbreeding rate can be considerably reduced ES S A S Eh B 2 Q vo z 5 of Va Q O 2 Inbreeding Relationship Number of generation Figure 1 Figure 2 Schematic connection between average Genetic gain with the two different selection genetic relationship and genetic gain Strategies in figure 1 e A Only focus on genetic gain e B Focus on both genetic gain and average relationship in next generation Side 4 af 41 Your complimentary use period has ended Interface User Manual Thank you for using PDF Complete VERSITET feed Features k i ic gain with a simultaneously control of the rate of inbreeding i in i the breeding scheme The programme is a further development of methods developed by John Woolliams Robin Thompson and Brian Grundy all Edinburgh where it was shown that both genetic gain and degree of inbreeding can be described as functions of genetic contributions Optimising genetic contribution for each sire and dam thus allows for a simultaneous consideration of genetic ga
9. Danish language file Plugins This folder may in future versions contain different Eval plugins A plugins is a small extension to a program or operating system cf footnote in Mnstallation gt Prerequisite gt Software0 paragraph For now this folder is empty and should remain empty Projects This folder contains all your projects and two additional projects The ADefault amp project is a project that Eval always start using unless you have selected another project at start up The other project is the fExample0 project which you may use to get to know the Eval program with some real data installed It is possible to restore the example project by copy the contents of the Eva interface 1 3 08 Documents eva Example0 folder to the Example project folder How to install the Eva Interface Side 9 af 41 Your complimentary Hj use period has ended _ amp Interface User Manual Thank you for using PDF Complete FEAR fed Features the Eva and Eva Inbred interface program Eval or received it via mail or on a CD ROM the installation procedure varies a bit The difference is mainly in how you save and locate the Eval installation file and how you start the installation Follow the procedure below to get the Eval installation file located or saved to disk then read the AlnstallingO paragraph below to do the actual installation of the Eval interface Using a CD ROM Use the procedure below if you received the Eval
10. at the encircled places image to the right is distorted to minimize size Adding a data file to your project Advanced parameters Crossover probability aro oO OE E EEE EEE REII SSS PE SPELEPAP EP EPAPER EA ALAA AAAA AAAA AA ENGE 555554 EE EE EEE ARAR ETEN ETE DFOJELEL TVILE AN brt POEA asese LookIn C Projects C3 clsep05_0 1 3 Default File Name C Programmer Eva Interface 1 3 02 Projects Giraffes Files of Type v cm File Run Project Help EVA EVA Inbred ea parameters Side 31 af 41 Your complimentary use period has ended Thank you for using PDF Complete VERSITET dl Features menu element 2 Click Data file yand the open data file window appear 3 Browse to where your data file is located and click the NOpen button Remember that your data file should have the extension Mato If your data file has another extension rename it and add it to your project as described above You are now ready to changes settings to your specifications and run Eva or Eva inbred Running Eva or Eva Inbred To run either Eva or Eva Inbred select either the AEvaO tab or the NE va Interface User Manual g EVA Interface ver 1 3 02 Update 1 Girraffes area 70123 v1 File Run Project Help New project Ctrl N Save Project As Ctrl V Save
11. complimentary use period has ended amp Interface User Manual C om 0 ate Thank you for using PDF Complete WMITKTETE aed Features SONOS seeme Utd as described by Sigurdsson A amp Jonmundsson J V 1994 Proceedings of the 5th WCGALP vol 17 140 143 and MacCluer J W Boyce A J Dyke B Weitkamp L R Pfennig D W amp Parsons C J 1983 Journal of Heredity 74 394 399 In version 1 3 added computing genetic contributions of base animals to the last generation and the possibility of computing genetic contributions and additive relationship between selected animals as given in the input file inbred prm see below In testing for the next version Average relationships between groups of animals computed with the algorithm proposed by Colleau J J 2002 An indirect approach to the extensive calculation of relationship coefficients Genet Sel Evol 34 409 421 EVA Algorithms Evolutionary algorithm Evolutionary algorithms are a class of algorithms based on biological evolution For a thorough description of evolutionary algorithms see Michalewicz 1998 For details on algorithms used in EVA see appendix A and B Input to EVA and EVA_Inbred cf MData Input to Eva and Eva InbredQ page 16 above EVA Inbred Parameter files Filenames for input and output files are supplied in a file given in the command line e g eva_inbred filename where filename is optional and defaults to eva_inbred_filenames prm In this file f
12. installation file on a CD ROM The following procedure below applies to both DVD and CD ROM drives You need to be aware of which drive you placed the CD ROM if you have more than one drive Overview 1 Insert the Eval CD into your pe CD ROM or DVD drive 2 Start the windows Explorer 3 Browse to the CD ROM or DVD where you inserted the Eval CD 4 Click on CD ROM or DVD drive 5 Double click the Eval zip file in the right part of the Windows Explorer window 6 Double click the Eval exe file when your unzip program starts Details Right click OStartO button and select DN ere DN DN x7 Abn ae Command Prompt Here Seg W Scan for viruses Add to archive Add to Menuen Start rar Compress and email Compress to Menuen Start rar and email Egenskaber bn mappen Alle brugere H Start Gennemse mappen Alle brugere ad gt zip or exe is the extension of a file name sort of a surname to a file unzip is the process of decompressing a zip file 7 Name of explorer depends on you language in Danish it is called fStifinderO and in English it is called Explorerd also please note that the screen dumps are made one a pc with a Danish version of Windows XP Side 10 af 41 use period has ended amp Interface User Manual Thank you for using PDF Complete VETETEIN where you placed the CD Click on the drive and double click the Eval zip file in t
13. menu you can save as print or change properties of the chart To move a chart to another application do the following Select the chart you want to move Right click click with the right mouse button on the chart and choose Save As from the menu Save the chart to a known location on your operating system Start or select the other application where the chart should be move and choose paste or insert usually from the Edit menu Project management Project management in Eval is the practice of organizing your Eval computations and settings in sets such that they are easily found and reloaded for further manipulations and computations Although Eval does not force you to organize your settings and computations in project we recommend that you do because e You may need the settings and computation at a later time and do not want to setup and load data files again e You may need to move the settings and computations to another computer at a later time and this is considerately easier when the settings and computations is saved in a project because the settings and data files is locate in one project folder e You may want to present results from a computation at a later time or need the computation results for some documentation at a later time e You may need to try different settings on the same data and you can do this by using different projects for each tryout e Etc Project Naming and Description Side 28 af 4
14. to all the graphically settings of the chart including colouring title legends etc The Save as Omenu is for exporting the chart either as an image which you then later can import in another application such as Microsoft Words cf ACopying output data to another applicationQ below The fPrint Omenu item is for printing the chart directly to a Auto Range gt ens _ standard printer O You can try to play around with the different menu items to experience To format the graphical presentation of the chart click the Properties Omenu item which activate the chart Properties From this window it is possible to change chart title font and colour in the ATitleOtab and by clicking the MLegendOtab it is possible to change chart line types and colours To change the title of the x an y axis click and the MPlotOtab which gives you access to formatting of the axis as well as the appearance of the axis 16 Right clickingOis done by placing you mouse point over the chart and them press the right button on your mouse Side 27 af 41 Your complimentary use period has ended h Interface User Manual Thank you for using PDF Complete VERSITET fed Features a application The Eva Interface has not as such the capability to organise computation results in a single document with all data and charts presented but you may easily copy most of the calculated results Text an
15. you can try if your computer has limited amount of memory installed In this folder you will also find a file called ME val error collector bata This file is meant to be used whenever the Eval interface program stops working during use or start up cf MFailures and possible solutions Documents The Documents folder contains three subfolders fevaO and fEvalQ The two first folders contain documents in relation to the development of Eval and some data you can use to restore the installed Eval Example project cf fFailures and possible solutions0 The third folder is where your user documents are placed among others the document you are reading Furthermore there is a couple of data file in the feva data zipOfile which you can study to see how the Eva and Eva inbred data file format is organised or use when experimenting with Eval Eva Eva folder contains the Eva and Eva inbred programs and a file with the default Eval parameter values YOU SHOULD NEVER USE OR CHANGE THIS FOLDER If you for some reason corrupt override or destroy the folder or the files in the folder then Eval will not run The only way to fix this failure is to reinstall Eval cf Failures and possible solutions This Folder contains help files and document files used in the Eva Interface application Which 1s available from the help The Language folder contains language translations for the Eval application Currently it contains an English language file and a partial
16. 1 Your complimentary use period has ended t Com p ete OOF Completa Interface User Manual VERSITET a Features J aOmay be just fine for a project you work on today and never more it poses a problem ifs you in say two years from now want to find that project again The above project name does not indicate what animal data or which settings was used so in Fields you must provide fact from the project name you would never ra ones guess that this project might concern a population rome tan r of 200 giraffes from area code 70123 and first Description ee settings tryout _a or some other animals and settings The point of this little example is that you should Default project filenames consider the naming of your project very carefully such that you at a later time are able to find the project again with ease A better name for the giraffe amp project would as an example be MGiraffes area 70123 version 10 and then describe the specific population size and parameters change in the project description You should use the project description because even the best project name may not include as much specifications as needed in a reasonable short project name Another point of adding a description to your project is that description is viewable in the project catalogue when the projects catalogue is enabled cf FProject Catalogue InbredPanel EvaPropertiesPanel Y
17. 941 0 0000 1 0000 1201990 0 0 1942 0 0000 1 0000 82428 0 0 1945 0 0000 1 0000 23057 0 0 1946 0 0000 1 0000 At the end of the file a summary statistics of the pedigree and its coefficients of inbreeding are written Largest genetic Max_gc txt A list of the 50 largest genetic contributions as shown below contributions Largest genetic contributions Ancestor Group N Group Add rel Gen cont 82177 2004 62 0 133540 00 120744 17001 2004 62 0 122268 00 107664 82010 2004 62 0 107369 0 107369 82097 2004 62 0 121759 0 090486 Relationships Gencont txt A list of genetic contributions and additive genetic relationships as specified in the parameter file FE adrel Additive genetic relationship gc Genetic contribution Ancestor Descendant Group N Group Add rel Gen cont 1300058 0 1137 0 000000 0 000000 1201990 1137 0 000000 0 000000 82428 1137 0 039812 0 039812 23057 1137 0 000000 0 000000 23713 1137 0 000000 0 000000 0 0 0 0 4 The AFilenamed specify what the result file is called in the project folder on your disk Side 25 af 41 Your complimentary use period has ended Thank you for using Com PO e PDF Complete Interface User Manual VERSITET ard Features The following is a short introduction to how computation results are presented in the Eva Interface and how you can make your own custom graphs and format the graphs to your specific need To view the results from a computation click the MResultsO t
18. A The two programs and their use are EVA inbred Computes inbreeding coefficients generation coefficients pedigree completeness indices genetic contributions and additive genetic relationships between animals EVA Computes optimal genetic contributions given a cost of inbreeding and proposes a mating list based on minimum coancestry matings With EVA_inbred a population can be thoroughly described in terms of inbreeding Pedigree completeness generation coefficients genetic contributions and relationships With EVA proposals for new matings can be obtained which maximize a function F w c w c Ac c genetic contributons to be optimised estimated breeding values A numerator relationshp matrix W Scalar weight on ebv input Wa Scalar weight on average relationship input EVA inbred algorithms EVA Inbred is a program to calculate inbreeding coefficients and generation coefficients for a pedigree of any size The program is based on the algorithm described in MEUWISSEN THE amp LUO Z 1992 COMPUTING INBREEDING COEFFICIENTS IN LARGE POPULATIONS GENET SEL EVOL 24 305 313 The program renumber the animal identification to consecutive numbers using a bit tree This will run quicker if the input file is sorted by half and fullsibs Animals with both parents unknown are the base population Generation coefficients are 1 in the base population Side 37 af 41 POE Your
19. Project Ctrl S Import gt Exit Look In 3 Projects v Ga A Ej oa dsep05 0 1 Ca Default Ca dfafF Example Ca Giraffes test File Name Files of Type Eva data files dat x g EVA Interface ver 1 3 02 Update 1 Girraffes are Fie Run Project Help InbredO tab in the top of the Eval window Please note that before you EVA EVA Inbred can run Eva Inbred you need to add animal contributions cf Eva Data parameters Inbred Parameters Running Eva compute breeding scheme Weight relationship Number of matings I Click the Run EvaObutton in the bottom of the Eval window and the Eva progress window become visible where the computation status is shown Eva running Current run started fi2 april 2007 12 31 31 CEST Current runtime 00 00 00 05 Please wait Eva is running Output from current run 2 Wait until the computation is finished which is indicated when the fCloseO button become enabled colour shifts from greyish to black or click the Abort O button to cancel the computation Please note that it may take a while before the computation actually stops Running Eva Inbred computing inbreeding 1 Click the Run Eva InbredO button in the bottom of the Eval window and the Eva progress window become visible where the computation status is shown Sid
20. a on your computer Java is a small system plugin that allows you to view java contents on the internet or run Java application on your computer The Java plug is easy installed via the Internet go to this page to install the Java plugin Click Free Java DownloadO button and follow the instructions given by the installation wizard Your may need to reboot your computer after the installation finished Please note that your pc also needs a program to extract zip files Most pcG has the ability to manage zip files but if yours do not then you can get one here http www winzip com Just download the Winzip program to a folder then browse to the folder after the download has finished and double click the downloaded file This should install the Winzip program If you encounter any problems installing Winzip please look at the website to get help Your pc is now ready to install the Eva Interface application Hardware We recommend using a stationary PC for computations on large populations but you may use a laptop for small population or the examples presented in this document The border between using a stationary pc or laptop is rapidly changing so you have to make you decision based on your laptops hardware and the time your computations take The recommended stationary pc has the following specifications 2 51 3 0 GHz processor or higher ik Minimum 128 Mb of ram Depend on population size in data file We recommend at least 512 M
21. ab in the bottom of the Eval for either Eva or Eva Inbred FF ses Text presentation All results and logs are as standard present in raw text You can access the text presentation by clicking text presentation tab in the top of the result presentation 1 It is possible to copy the raw text to other application by doing the following steps 1 Use you mouse pointer and click somewhere in the text presentation window 2 Press the fCtrlO key on the keyboard and push the FAO key to select all text in the window 3 Press the ACtrlOkey and push the NCOkey to copy the text 4 Open the program where you wish to move the copied text and insert the text Table presentation In addition to the text presentation most of the results are also presented in data tables To access the table presentation if present click the tab in the top of the results window Table results are presented as columns and rows as shown here Animal Sire Dam Sex Group F 11300058 Oooo 0 0 1941 0 0 l 11201990 1942 0 0 182428 0 0 0 1945 0 0 oOo oOo oOo If you wish to copy the result table presentation to another application then follow the same procedure as when copying text results It is possible to copy the table presentation directly into Microsoft Excel this way but please note that the column header are not included in the copy Chart diagram presentation Most of the results with a table also have a line chart diagram presentatio
22. ametersO in the Eva Interface User Manual These parameters are given as a Fortran90 namelist amp evaparm Parameter x parameter x where parameter is one of the parameters specified below and x is the value given If a parameter is not given it takes a default value also given below Alg gorithm parameter Description Default value population size in the evolutionary algorithm n_offspring Number of offspring per generation in evolutionary 10 algorithm Number of generation to run algorithm 1000 restart_interval Number of generations without improvements before 1000 mutate_probability is increased to 0 5 and a new population created from the present best solution exchange_algorithm Interval in generations between running the exchange 100 algorithm mutate_probability mutation probability in evolutionary algorithm a directed mutation pr Probability of exchanging parent with fbestO 1 nmatings obability alternative crossover_probability crossover probability in evolutionary algorithm Seed_rng Seed for random number generator If 0 the number of seconds since midnight is taken as seed Example amp evaparm popsize 10 generations 100 n_offspring 10 restart_interval 1000 exchange algorithm 10 Output from EVA cf Results from Eva and Eva InbredQ page 22 above Output from EVA_inbred cf Results from Eva and Eva InbredQ page 22 above Side 40 af 41 PDF Complete BREDE Featu
23. b of ram ik At least 15 Mb free disk space Even with a computer of this size Eva calculation may take hours The time consumption is however depending of how large a population you have in the data files and how parameters are specified As an example we ran Eva on a data file with a population of 24 500 animals on a computer with the above specifications and it took 20 minutes You should not take this general example as a guideline for how long time the Eva programs need for a calculation because the algorithms used in the programs are stochastic which indicate that the complexity of the calculation is exponentional in the size of the population A plugin is a small system extension that allows you to run or use other technologies than originally installed on your computer such as viewing Shockwave flash Java or QuickTime animations videos in your Internet browser but also such that you can run programs developed in other technologies as standard Windows applications Zip files are a type compressed files that can contain multiple other files Sort of a container library that needs to get uncompressed before their contents can be used Winzip is atrial program which you can only use for a short period of time usually 30 45 days There are other freeware programs that can manage zip files Which one you prefer is entirely up to you Side 7 af 41 Your complimentary use period has ended Thank you for using PDF Compl
24. ce Version O 4 Save installation file to a known folder drive You need to find the installation after the download has finished likewise you may need it later for doing a reinstall Start Windows Explorer when the download has finished cf Using CD ROM bullet 2 Browse to the folder where you saved the Eval zip file rer GemOin Danish Side 12 af 41 Your complimer use period has en Thank yoii foru the right part of the Windows Explorer window 8 Double click the Eval exe file when your unzip program starts Details Start your Internet browser and go to Eva Interface download page http eva agrsci dk Locate the download link and click on the link After a while a download window appears Please note that the image of the website may not be up to date On the Internet it looks like this To download click the Saved button When you click the MSaveO button a new window appears where you can browse to the location where you wish to save the installation file as the next image shows Browse to the folder where you wish to save the installation file and click the Saved button you must be able to find this folder again EVAI 13 Microsoft Internet Explorer Filer Rediger Vis Foretrukne Funktioner Hj lp Q Tilbage v gt v ix GE Er g Er Adresse la http eva agrsci dk EVA Interface 1 3 Download page This download page is only intended for persons
25. d are in standard DOS 7 bit ASCII format and the results are formatted e ke Project name Pefaut with a space character dividing each result column such Es that they can be imported into Microsoft Excel or other applications The files are located in the project folder Pedigree completness Results Description of Eva Results Eval Tabname Log file Eva log EVA prints a log file The file contains information on the parameters a description of the population and the iteration history Convergence of the Eva conv txt Contains convergence of the population of solutions population of solutions solution solution variables and in the rest of the lines in the ASCII file l The Eval Tabname0 actually specify what is printed on the result tabs in the Eva Interface A result tabs is a Results graphical element in the user interface that looks like this The AFilenamed specify what the result file is called in the project folder on your disk Side 23 af 41 Your complimentary use period has ended Thank you for using PDF Complete Interface User Manual VERSITET contains the animal information The first line of the file is formatted as a comma separated list with the following column names Sire Dam N mating Nm Nf m EBV F vF Sire txt Dam txt and followed by a line per matting as shown in
26. d tables presented in Eval to other applications on you computer As already explained in the Presentation of computation resultsOchapter you can do this by using your operating system s default shortcut keys As an example on the windows operating system by pressing the Ctrl and A keys Ctrl A at the same time you select all text in the currently focused result If you then want the selected result copied to another application you press the Ctrl and the C keys Ctrl C at the same time Now the selected result is in a clipboard shared among all applications on you computer Now if you want to insert the result you have copied to the clipboard do the following Open the application you want the result to be placed in and press the Ctrl and V keys Ctrl V at the same time and the result should appear in the application If the copied result does not appear in the other application you have missed or made a mistake during the copy action try following the above procedure again The procedure is similar on other operating system although the key you use may vary While the above procedure is fine for text and tables it will not work with the generated charts To move the charts to other application you need to save the chart as an image file and then insert the image into your other application All the charts have a right click menu which means that if you click with the right mouse button on the chart a small menu will popup From this
27. e 32 af 41 a Interface User Manual ss Mirese shed which is indicated when the NCloseO button become enabled colour shifts from greyish to black or click the MAbortObutton to cancel the computation Please note that it may take a while before the computation actually stops Examples To help understanding the use of Eva and Eva Inbred two data sets will be provided at the course Jutland Horse The first data set 1s from The Jutland Horse The Herd Book of the Jutland horse 1s old and therefore pedigree information on this breed is very complete Another characteristic of horse breeding is the quite long generation intervals This dataset include 3433 animals The oldest of the animals are born in the early 1890G Out of these animals 886 are assumed to be breeding mares and 35 are breeding stallions The remaining are pedigree animals or younger animals The Jutland Horse is Denmark s national draft horse It was developed from a heterogeneous herd of horses found in Jutland around the middle of the 19th century The Jutland Horse is a medium to heavy breed with great depth of girth strong limbs powerful movements and a good temperament In the majority of cases its colour is red although occasionally brown and black individuals occur Each year about 250 mares are served by about 25 stallions and approximately 100 foals are registered annually Registration and studbook records are maintained by the National Department of Ho
28. e correct set in the log files in the runtime dialog I think I have corrupted Stop Eval if it is running Then to restore the example project the Example project and installed together with the Eval installation you copy all files in would like to restore it the ME va interface 1 3 02 gt Documents gt eva gt Example folderOto the fE va interface 1 3 02 gt Projects gt ExampleO folder When asked to override the existing files click AYesQ Please note that doing this will indefinitely destroy the original Example project I did not find a solution to e Use the ME val error collector bat amp program located in the ME va my problem interface 1 x xxOfolder to get a trace of the failure and send the Side 35 af 41 Your complimentary use period has ended Interface User Manual Thank you for using PDF Complete VERSITET REE d Features 02 Ofile to one of the contact mails To use the program just click twice on the NE val error collector batOfile Then the Eva Interface starts After Eval has started replay the actions you took before Eval stopped and then send the f rror logOfile to us together with a description of the actions that made Eval stop working what you did in the program before it stopped workin Latest changes Version 1 3 08 Only changes to the internals working of the Eva Interface has been done is this version and a new release of the Peer Bergs Eva program is added to the In
29. e data file for all animals to be used in the Eva inbred contribution generator Eva Parameters The following descriptions are a small explanation of the different parameters used in the Eva Interface The parameters are divided into two groups Basic parameters and advanced parameters where you will use the basic parameters for 99 of the time and rarely use the advanced parameters Put another way Do not use the advanced parameters unless you know exactly what they mean and what they do Basic parameters Parameter Description Weight relationship The weight to be put on average genetic relationship within the group containing the suggested matings and the other animals being able to contribute to future generations Since we want to reduce the future rate of inbreeding this weight has to be negative Due to the Side 19 af 41 Your complimentary use period has ended Interface User Manual Thank you for using PDF Complete WITKTE EE feed Features small variance of average genetic relationship this weight is often numerical much larger than the weight put on merit The weight to be put on average merit of the suggested matings Due to quite large variation on merit compared to variance on average additive relationship this weight is much smaller than the weight put on average additive relationship Number of matings This figure tells how many matings you want the calculation to suggest In a cons
30. ecinssaeceoeetetieoneeneet 36 Appendix A Eva and Eva Inbred Documentation 0 0 0 0 cece cccce cece rese caaeecaaeceeeeeeeeeeeeeeesseeeeees 37 Introduction This document is a guide to the use of the EVA Interface program Eval which is a graphical user interface GUI for the two programs EVA EVolutionary Algorithms and Eva inbred researched and developed by Peer Berg We aim to guide you through the different parts of Eval and give you some background knowledge about how the program works Specifically you will learn how to manage projects how to add data files to project and how the different parameters values will influence the result of a computation of a project Furthermore we aim to discuss and assess the results from the Eval computation To facilitate the guidance we present two project examples One based on pedigree information for Jutland horses which have very long generation intervals and excellent complete pedigree information The other example is based on information from Danish black pied pigs which have short generation intervals and poor pedigree information Please note that this document does not examine or present arguments for the algorithms used by Eva and Eva inbred To get a more indebt discussion of the algorithms used by EVA and Eva inbred please examine the original EVA and Eva inbred documents which you can download from our homepage at http eva agrsci dk cf AAppendix A Eva and Eva Inbred Documen
31. eeding value Predicted breeding value e g BLUP of animals breeding value Real Text Optional field with a text string of up to 15 characters to be printed in the mating list Regarding Animal ID then consistency is of utmost importance Sometimes animal ID for one or another reason changes or is prolonged with one or more digets Such changes are not always done throughout the pedigree In some cases the changes is only done for the animal itself and not in the situation where the animals is sire or dam of another animal In that situation the program is unable to recognize the correct sire and dams If the Animal IDG are changed with two digets in front telling which region the animal is from without doing so for the Sire ID and the Dam ID then the link are missed which can be seen below If sire or dam are unknown the sire or dam fields in the data input file must be marked with a 0 zero to indicate that either sire or dam are missing Side 17 af 41 PNF use period has ended Thank you for using O m p ete PDF Complete Your complimentary R Interface User Manual VERSITET aed Features a Broken Links Sex need only to be specified for potential parents animals with Max matings gt 0 Birth time can be specified within month years or another time period When the input data is going to be used for Eva inbred analyses the data have to be sorted by the b
32. else HTML Mi 3 attached Eval installation file Click with Filer Rediger Vis Inds t Formater Funktioner Handlinger your right mouse button on the attached Hj lp file and click Save as 0 Ga Besvar G Svar til alle 3 Videresend G Ga Y X Fra Jes Nielsen Sendt ti 13 03 2007 13 18 Til Jes Nielsen be Emne Eval Installation file Vedh ftede filer ma va bn Hi Udskriv Gem som This is the Eval installation file you requested Fjern Kind regards Kig Jes Nielsen Kopier Set nd Marker alt Browse to a known folder you need to Gem vedh ftet fil 4x i emi bm H vi X Ca i v Funktioner be able to find this folder again in the GE Ah eV en Windows Explorer Click the fSaved PE button dokumenter 3 Skrivebord Dokumenter Denne computer Filnavn Eval _1 3 02_Update_2 zip v eee Fe Alle filer z Annuler Please continue the installation by reading the AlnstallingO paragraph below Using the Internet Use the procedure below to download Eval from the Internet Please note that how you save the Eval installation file to disk may vary depending on which Internet browser you are using The following procedure is base on the use of Microsoft Internet explorer but if you are using Mozilla Firefox the procedure is pretty much the same Overview 1 Start your Internet browser 2 Go to Eval download page http eva agrsci dk 3 Click MDownload Eva Interfa
33. ely by clicking the fiNext gt gt gt Obutton This starts the Eval project catalogue where you create a new project by adding the project specifications You need to at least supply a project name and a project path but as Default project filenames InbredPanel EvaPropertiesPanel indicated in the Project naming and descriptionO paragraph it is recommended to supply a meaningful projects description such that you are able to recognize the project some time in the future The project path you need to supply is actually a folder within the project folder as recommended in the MProject Folders ok I Cancel and PathsO paragraph By clicking Cancel in the project catalogue dialog or if you option to create a new project from the project catalogue and then click cancel Eval loads the default project Your first project In the next few paragraphs a short introduction to how you start Eval and making a project is presented Further we will show you how to either make a breeding plan or calculate inbreeding from the dairy cattle data in the default project Starting Eval How you start Eval depends on which windows operating system you use The following is based on the use of Windows XP but with hints to how to use another operative system such as windows 951 98 Side 30 af 41 Ed Features desktop The Eval icon is placed on your desktop after a successfully Eval ins
34. ervation population it will be advisable to use the number of litters born per Weight merit year or time period Allow repeating matings In far the most cases it will be best to allow repeated matings If you want to put restrictions on the number of offspring from a potential parent it is better to regulate this in the Eva input data via the variable Max matings for specific parents The balance between the weight on additive genetic relationship and the weight on merit was discussed on page 5 in this document under Balance between genetic gain and additive genetic relationship The image below shows the Eva Interface with the Eva parameter tab selected The basic parameters are in the upper half of the window in the group box MData parametersO and the advanced parameters are in the lower part of window The advanced parameters values shown in the image below are the default parameters Side 20 af 41 Your complimentary use period has ended Interface User Manual Thank you for using PDF Complete VERSITET feed Features File Run Project Help EVA EVA Inbred Data parameters lt Weight merit Weight relationship Number of matings Allow repeating matings Reset parameter values E r Advanced parameters Restart interval 1 000 Crossover probability i 0 1 2 Number of offsprings i 10
35. ete a Interface User Manual VERSITET Before we start to do the exact installation of Eval we would like to give a few advises about where to install Eval First of all it is not a good idea to install Eval on a network drive because Eval need to transfer a substantial amount of files between the application and the hard disk drive because it needs to read your data file Eva input file which may be very large into the Eval application for use and it needs to output result files from your computation to hard drive Furthermore if you install Eval on a network drive the risk corrupting the project and project catalogue files are significantly increased because of network connection failures and time deviation between your local computer and the network drive The short conclusion of the above advise is to install on your local hard disk drive usually C or D because this avoids many small problems and easily your use of Eval You should however always backup the Eva data as well as you other important data on your local hard disk drive periodically to avoid loss of data If you later need to reinstall Eval then your project files should not get influenced by the reinstallation procedure cf MFailures and possible solutions Recommended installation folder In what folder is Eval then best installed The best installation folder for the Eval installation is entirely up to you but please install Eval in an easy accessib
36. g filled out but often it is convenient to fill this column out especially if the Animal ID is a large number without any meaning to you In that case the text column can be filled with the name or the herd book number of the animal The Eva input file can be stored any place on you computer but when adding the data file to a Eva Interface project the Eva Interface will copy your input data file to your project folder If the original input data files are stored in a general catalogue it is of utmost importance to use well defined names for the data files e g WutlandHorse_06_fullped datO instead of only fhorse060 The advantage of a general data file catalogue is that many input data files may be used in numerous projects Data file example Although the example below is shown in a table format it amp not how you should actually generate the input file First of all there should be no naming of each column header secondly each column value is actually separated by a space character The table is only meant to show you the data file fields and possible values Side 18 af 41 Your complimentary use period has ended t i Thank you for using Com p e PDF Complete Interface User Manual VERSITET Animal ID SireID DamID Sex Birth time Max matings Breeding value Text 983 0 0 1 1997 0 8 trojan 25925 899 909 2 1997 0 8 125489 0 0 2 1998 0 8 992 0 0 2 1998 0 8 290268 0 0 2 1999 0 8 480792 290268 125489 1 2005 10 8 Zeu
37. he Eva Interface In addition the Eva Interface gives you the possibility to organise your data files parameters files and result files in projects such that they are easily loaded at a later time for further experimentation or manipulation FORTRAN is a computer programming language with strong mathematical functionality Side 5 af 41 Your complimentary use period has ended Interface User Manual Thank you for using PDF Complete F TTER Sead Features Parameters Project Eva Interface Project management Result presentation results results Result files Result files Eva Eva_inbred The different parts of the Eva Interface application are e Eva Interface Eval Manages projects data files pedigree trace files result files and handles parameter file generation for the two Eva and Eva inbred applications and present computation results for the user as tables and graphs e EVA Future rate of inbreeding is dependent additive genetic relationship among the animals within the breeding population in next generation EVA computes optimal genetic contributions of potential parents given a cost of inbreeding and proposes a mating list based on minimum coancestry matings The calculations are based on estimated breeding values for the potential parents and pedigree information from these animals and earlier used animals within the po
38. he right window Cf PrerequisiteO Tilbage h gt gt Bj re S g T Mapper lay i xX Adresse b FA Mapper Navn E Gkriebord a I Eval 1 3 02 Update 2 zip GB Dokumenter c W Denne computer H 31 diskette A sa Main C s Development D lt 2 DVD drev E gt DVD cd rw drev F Please continue the installation by reading the AlnstallingO paragraph below Using Mail Use the procedure below if you received the Eval installation via email Please note that how you save the Eval installation file to disk varies a lot depending on which email client you are using The following procedure is based on the use of Microsoft Outlook but if you are using Outlook Express the procedure is pretty much the same Overview 1 Open the email you received 2 Click with right mouse button on Eval zip file and click Save as 3 Save attached file to a folder you know how to find You may need the installation file later during a reinstall 7 Start the windows Explorer cf Using CD ROM bullet 2 4 Browse to the folder where you saved the Eval zip file 5 Double click the Eval zip file in the right part of the Windows Explorer window 6 Double click the Eval exe file when your unzip program starts Details 8 Save as 0is the same as Gem som in Danish Side 11 af 41 use period has ended p Thank you for using fd Features re gt Eval Installation file Meddel
39. ical element in the user interface that looks like this sm Side 24 af 41 POE Your complimentary use period has ended h Interface User Manual om D ete Thank you for using PDF Complete EJIE C A Features ves information on data and average inbreeding by birth time avg F Average inbreeding coefficient max F largest inbreeding coefficient avg coa Average coancestry incl self F ST Expecte kler under random matin f IS Deviation from random mating Wrights f is PCIN Pedigree Completeness Index for n generations Gencoef Average generation coefficient Group N N inbred avg F max F avg coa F ST f IS PCI 4 Gencoef 1941 1 0 0 0000 0 0000 0 5000 0000 0 0000 0 0000 1 00 0 0 0 0000 0 0000 0 5000 0 0000 0 0000 0 0000 1 00 0 0 0000 0 0000 0 5000 0 0000 0 0000 0 0000 1 00 0 0 0000 0 0000 0 1250 0 0 0000 0 0000 Inbreeding F_coeff txt A file with one record for each animal in the same format as coefficients in the input file with each record extended with the inbreeding coefficient and the generation coefficient of the animal Birth time Integer Birth year code or equivalent from input file Inbreeding coefficient real between 0 and 1 real Generation coefficient real gt 1 Inbreeding coefficient Generation coefficient PECn Pedigree Completeness index in n generations Animal Sire Dam Sex Group F GEN 1300058 0 0 0 1
40. il then Download the new version of Eval from the Internet as described in the above paragraph cf Using the Internet Then use either procedure 1 or procedure 2 described below Update procedures 1 Install directly in PoldOEval folder a Browse to folder where you saved the updated version of the Eval installation file b Double click the Eval zip file in the right part of the Windows Explorer window c Double click the Eval exe file when your unzip program starts d Change the default installation path to the path where the old version of Eval is installed Click browse and locate the old installation folder and click NOKO EE Installation of Eva Interface 1 3 02 Update JE xd Please see How to Install on website http eva argsci dk Destination folder n Browse astallation progress e Click Install f Follow the instructions given by the installation program 2 Install to new folder and copy projects more secure Browse to folder where you saved the updated version of the Eval installation file Double click the Eval zip file in the right part of the Windows Explorer window Double click the Eval exe file when your unzip program starts Follow the instructions given by the installation program The Eva Interface must not run during the next steps Start the Windows Explorer cf Install Browse to old Eva Interface installation folder Right click AprojectO Click on fCopyO Browse to the
41. ilenames are given in a namelist format e g amp files file filename The following filenames can be given with default values also given File description Data file Log file File with inbreeding coefficients Default filename Summary file Genetic contributions Largest genetic contributions Parameters to compute genetic Fcoetf file F_coeff txt F_summary txt Fsummary_file Maxgc_file Side 38 af 41 POE Your complimentary use period has ended p Interface User Manual C om et e Thank you for using p PDF Complete VERSITET Generations to compute Pedigree Pci_ngen 3 Completeness Index Example amp files datafile Grdm1970 a datO fcoeff_file Ordm_f txtd pci_ngen 5 Filenames or parameters not given has default values If no filename is given when calling eva_inbred and no default eva_inbred_filenames prm file is found all parameters take their default value as given in the table above To compute additive relationships between animals and genetic contributions from an ancestor to a descendant supply a parameter file named by gcparm_file above containing in each line amp contrib ancestor id1 descendant id2 group idg where at most two of the three arguments need to be specified id I is the id in the pedigree of an ancestor 0 if all base animals id2 is the id in the pedigree of a descendant idg is the id of a group of animals in the pedigree file if idl a
42. in and rate of inbreeding The programme puts weights on the average relationship among the selected combinations and the previously used animals in the breeding scheme and on the average breeding value of the selected animals In principle a variable S 1s generated S bl average breeding value b2 average relationship where bl is the economic value of a breeding value unit and b2 is the cost of inbreeding Depending of the weights chosen EVA finds the particular use of the potential parents which optimise the variable S and thus the breeding scheme As the average relationship of a particular candidate to the group of selected candidates changes depending on the set of selected candidates the S value also change Therefore complex calculations are needed The selected matings are printed on a mating list It is difficult to specify the weights bl and b2 and it depends on various subjective estimates The literature gives however methods describing functions to specify these weights The value of the genetic gain the chosen time horizon as well as the cost of the inbreeding depression all form part of these functions Again it 1s a subjective estimate which time horizon is to be considered The longer the time horizon is the lower weight on the genetic gain and the higher weight on relationship The reason for that is that the genetic variation will be reduced with inbreeding and the longer time horizon considered the more important
43. in the left part of aaa the window all available animals are listed and to the left is a list for the animals you Available animals Selected animals Please note that sorting of items in Available Items and Selected Items lists select to get included You move an animal are done lexicographically on strings not numbers even though you have ae Vi hes ec ee that r ve same although to the Melected animals list by Die ip nl Meche highlighting animals on the left and then click the f gt Obutton You may select individual animals by pressing the NCtrlO key while highlighting individual animals by Generate parameters clicking once on the animal id in the left list Alternatively you may move all available animals in the left list to the selected animals list by clicking the f gt gt Obutton It may not be possible to generate all combinations of the selected animals if you have a very large list of available animals because your computer may not have the required amount of memory to handle the number of combinations If the Eva Interface calculates that required memory is less than the needed memory it issues a warning like the following El The selected number of animals are 24501 The memory required on your computer to handle this number of animals may exceed your computers installed memory To insert 24501 animals will require 300161751 contribution lines Do you want to proceed Side 22 af 41
44. irth variable such that parents are placed in an age group before their offspring s You may for example use some kind of renumbering scheme as adding 5 to the offspring age and then multiply with 10 on all animals ages in the input data file such that offspring may have a 20075 1007 5 x 10 20075 age and parents have 20070 2007 x 10 2007 This way you will be able to decode the age groups back to the original number by dividing by 10 In Max matings the maximum number of offspring per potential sire or dam in the next breeding season Is given In an optimal setting this value is the biological maximal number of offspring but it can as well be the highest number of offspring wanted of a special parent If an animal is not to be used in a breeding scheme add a 0 zero in the Max Matings field to indicate that you either don t want offspring from this animal or that the animal is deceased The breeding value should be the breeding value used in the selection programme often a total merit index but it can as well be another breeding value or a phenotypic measurement In many conservation programmes no weight is put on breeding values meaning that Eva is used just to reduce the future rate of inbreeding as much as possible In that situation all animals can be given a dummy ebv eg 10 but not necessary the same value for all animals The text column can be filled if wanted The programs runs smoothly without this variable bein
45. it is to keep the inbreeding increase under control Another possibility is to choose the weights in such a way that a maximum rate of inbreeding per generation will not be exceeded The literature gives arguments that the rate of inbreeding should not exceed 0 5 to 1 per generation Eva Interface Overview As already suggested in the introduction Eval is at graphical user interface for the Eva and Eva inbred programs This indicates that you could use Eva and Eva inbred without Eval but to use the two programs without Eval requires that you have absolute knowledge of how the parameter files are formatted that description is beyond this manual The Eva Interface application is build on top of two FORTRAN applications Eva and Eva inbred developed by Peer Berg These are the applications that actually do the computation based on the parameter files you make through the Eva Interface The Eva Interface application functions as a mediator for you and Eva or Eva inbred by presenting you with a graphical user interface where you can manipulate the parameter files used by the underlying applications When you press the run button in Eva Interface the interface generates the parameter files for you and starts the Eva or Eva inbred application When either Eva or Eva inbred finish its computation the interface loads the results from a number of results files generated by the Eva or Eva inbred application and presents the results as tables and graphs in t
46. le folder such that you avoid searching and clicking through loads of folders before you locate the Eval projects folder Installed Folders and what they contain What folders are created during the Eval installation There are several folders created some of these you should not touch add or remove file from or to because it might crash the Eval application The folder structure created when installing Eval looks like the following Please note The numbers in Eva Interface 1 3 080 may vary from the ones on your computer El EG Eva interface 1 3 05 E i Documents i i eva G Doc HF G Example i Evai CI Eva FE help G Languages 3 Plugins EI E Projects i Default Example ED jy heste 5 sorte grise The following table presents a short description of the created Eval folders and their contents Side 8 af 41 Your complimentary use period has ended om lete Thank you for using Interface User Manual p PDF Complete VERSITET FEE Features Folder name Description Eva interface 1 3 08 This is the root folder of the Eval installation This folder contains all the executable files property files error log file and your project catalogue file The only two files that should mainly concern you are the fEvaW exeOand MEva jarOfiles fEvaW exeOis the Eval main executable file which you double click to start the Eval application ME va jarOis the alternative executable file
47. n of the result The charts may be a static specified or dynamically user specified A statically specified chart can not have the data presented changed but you may change header and legend on the chart In contrast with dynamically user specified charts you can change which data is presented in the chart and also change header and legends You view the charts by selecting the tabs with a I and some explaining text If a tab is present with the text FCustom diagram 0 fill Custom Diagram it means that you can select the data presented in the chart by selecting different data columns in the result table Use the following steps to make a custom diagram 1 Click on the result table tab The Ctrl key is placed on the keyboard at the lower left corner Side 26 af 41 Your complimentary use period has ended Interface User Manual Thank you for using PDF Complete VERSITET 7 Features to get presented in the custom diagram It 1S possible to select multiple columns by pressing the fCtrlO key on the keyboard and clicking on each data column you wish to include in the chart 3 Click on the custom diagram fi Custom Diagram and you should see a new with the data you specified In the following example we decided that the favg FO Average Inbreeding Coefficient was the only data column we wanted to be presented in the custom diagram g EVA Interface ver 1 3 02 Update 1 Exampl X g EVA In
48. nd id2 are both specified then both additive relationships and genetic contribution are computed if idl and idg is supplied then the average contribution and relationship of id1 to animals in group idg is computed if idl is not specified the contribution and relationship of all base animals to id2 or animals in idg is computed if both 1d2 and idg are specified idg is ignored Example amp contrib ancestor 0 group 2002 computes average genetic contributions of all ancestors animals with unknown parents to all animals in year group 2002 EVA Parameter files EVA can be called with an optional parameter specifying a file with parameters Eva parameter If a parameter is specified in the command line this should be a valid filename referring to a file containing parameters as Fortran90 namelists If a parameter is not specified parameters are read from the default parameter file eva prm The file with parameters for running EVA default eva prm has to be located in the current directory the directory where EVA is running Eva prm parameter file contains two sections one with parameters for the problem to be solved and another with parameters for the evolutionary algorithm Side 39 af 41 Your complimentary POE use period has ended Com plete stam a Interface User Manual VERSITET fed Features cf fEva ParametersO page 18 above Algorithm Parameters Also know as MAdvanced par
49. new Eva Interface location and click fi va Interface OTopmost folder ao of mu mo Parameters and results Data Input to Eva and Eva Inbred Input to EVA and Eva Inbred is provided in a data file with data and the Eva and Eva Inbred parameters are written directly in the Eva interface In the following sections the content of input files and the meaning of the different parameters are described Side 16 af 41 Your complimentary use period has ended Thank you for using Com p e PDF Complete Interface User Manual VERSITET SEE d Features The data file is an ASCH file with the following columns Animal ID Integer ID for animal Parents must be placed before their offspring in the data input file Sire ID Integer ID for sire of animal If sire is unknown the sire field in the data input file must be marked with a 0 zero to indicate that sire is missing Dam ID Integer ID for sire of animal If dam is unknown the dam field in the data input file must be marked Sex of animal 1 if male 2 if female Integer i Birth time Time when animal is born In units of time period Integer Max matings Maximum number of matings for an animal 0 if the animal is not available as a candidate Integer If an animal is not to be used in a breeding scheme add a 0 zero in the Max Matings field to indicate that you either don t want offspring from this animal or that the animal is deceased Br
50. p value e g to 2008 last year in input data file computes average genetic contributions of all ancestors animals with unknown parents to all animals in year group 2008 and will generate the maximum genetic contribution result Please note that his can only be done for the last birth time group Quick add 8 By animal ids By optional text Contributions generator Ancestor 0 Descendant o add z Ps if asv eihss tines uhia Side 21 af 41 Your complime use period has en Thank you for u PDF Compl meet the number of generations to compute pedigree completeness Index i in the Number of generationsO field in the pedigree completeness group box in the bottom of the window ea EVA Interface ver 1 3 02 Update 1 Example Fie Run Project Help EVA EVA Inbred Inbred Parameters Quick add By animal ids 0 By optional text Contributions generator me ost Contribution table ncestor A ad Delete selected contribution Select All Pedigree completness Number of generations Parameters Run Eva Inbred Project name Example Project path Projects Example If you prefer to use the contributions generator then activate it by clicking the NContributions generatorObutton found in the quick add group box in the top of the window This starts the following window picture to 16902 the right In the left list
51. pulation It is important to use all available pedigree information The contribution of the potential parents is dependent on the cost given to future inbreeding The average estimated breeding values is calculated for the fmatingsOas well as the average additive genetic relationship among animals which possibly will contribute to the future generations e Eva Inbred Computes inbreeding coefficients generation coefficients pedigree completeness indices genetic contributions and additive genetic relationships between animals With Eva inbred a population can be thoroughly described in terms of inbreeding Pedigree completeness generation coefficients which estimate the average number of generations with known pedigree genetic contributions from specified animals and relationships between specified animals Installation Prerequisite Software Side 6 af 41 Your complimentary use period has ended i Thank you for using Com PO e PDF Complete Interface User Manual VERSITET et on a Microsoft Windows operating system OS We recommend that you 1 install Eval ona 1 Micro soft Windows XP OS but it should work on Windows 95 and 98 as well although it may perform much slower and you will need to install a different version of Java The different version of Java can be found from same page as described in the paragraph below Before you can run the Eva interface program for Eva and Eva inbred you need Jav
52. res Original Eva User Guide by Peer Berg Danish Faculty of Agricultural Sciences Department of Animal Breeding and Genetics P O Box 50 DK 8830 Tjele Denmark E mail Peer Berg agrsci dk Michalewicz Z 1996 Genetic Algorithms Data Structures Evolution Programs Springer Verlag Side 41 af 41
53. rse Breeding Its breed society The Jutland Horse has about 250 members The greatest danger to its future survival lies in the limited possibilities open for the use of this heavy working animal Carlsberg has employed the Jutland Horse to pull beer wagons since 1928 and this brewery still uses it for marketing purposes The Genetic Resources Committee has drawn up a co operation agreement with the breed society Side 33 af 41 P C a Interface User Manual The other data set contains information on the Danish Blackpied Pigs This breed is characterized by scarce pedigree information and short generation intervals The dataset include 1726 animals The current population of Danish Black Pied Pigs originates partly from the old Danish landrace and partly from a limited importation of Gloucester Old Spot animals in 1930 The breed has never been widely distributed in Denmark because black pied pigs were unsuitable for the production of bacon The breeders of black pied pigs could not get their animals tested at recognized pig research stations and had therefore no possibility for breeding for good carcass quality Instead they bred for high fertility and good mothering characteristics The buyers of black pied gilts were mainly producers of baby pigs who valued their good nursing and hardiness characteristics By crossing black pied sows with white boars white progeny were produced whose poorer carcass quality was not immediatel
54. s 483055 159401 188336 1 2005 5 8 Bigblue ad 983 0 0 1997 0 3 trojan This is how the picture on the right the same 8 fs So 3 coe J data file looks in notepad There is no column 5337 2 2 Tee B 3 290268 0 Q 2 1999 Q 8 header and each column value is separated 480792 290268 125489 1 2005 10 8 Zeus 483055 159401 188336 1 2005 5 8 Bigblue with a space character Please note that some animals in the data file have been given an optional text in this case it the name of the animal but it could as well have been a herd book name or number The optional text is useful when you use the contribution generator in Eval because the optional text is viewable Please note the following in the above examples table above and image to the left O All parents are listed before their offspring and the file is sorted such that parents appear before the offspringG O Animals with Ids 983 125489 992 and 290268 have unknown parent indicate by a 0 zero in the sire and dam fields Likewise we don want to use these animals for breeding indicated by a O zero in the Max matings field In this case it is most likely that they have passed away but they might as well just not be suited for breeding It is of utmost importance that all sire and dam fields are linked to an animal ID in the input data file That means that you can not have a sire ID or dam ID without a matching animal ID O Optional text is optional but must appear in th
55. tall Jave above but EvaW exe e Check that your pc meets the requirements specified in the wond start prerequisite section of this document Try starting the Eva jar program instead found in the program folder The reason the EvaW exe may not start is that your computer have less memory installed than the MEvaW exeO program needs fEvaW exeOis optimized for speed and therefore requires more memory than the fEva jarO Eval doesn start after last Did you close Eval while it was running Then some of the data time I used it files that Eval uses may have become corrupt The easiest solution to this is simply to reinstall Eval Your projects should not get influenced when you reinstall Eval but make sure you take a backup of your project files before the reinstallation If you use the default project folder then your project are located in the Eval project subfolder Did you update Java or did you remove Java from your PC Then ou need to reinstall Java See procedure in prerequisite section The parameter values I Please be aware that numeric fields should be used with thousand enter in the program are separators to work correctly E g 1000 should be written 1 000 changed when I move to The example is using a dot as a thousand separators Danish another parameter field Which letters you should put as thousand separators depends on the country and culture your computer is installed with You should check that the parameter values ar
56. tallation on a Windows XP system If you can not find the icon the browse to Eval installation folder and locate the EvaW exe 2 Double click either the Eval icon on your desktop or the EvaW exe file in the Eval installation folder to run program Eval then starts If the program do not start EO data O Documents D Eva help please look in the FFailures and possible solutionO chapter below Creating a project p lt Click Filed A 2 Click ANew Project O A and the B window appear 3 Fill the NAuthoro Project Named and MDescriptionO fields with proper information cf MProject managementoO 4 Click the fBrowseO button to select or Description Run Project Help New project Ctrl N Oper EL San cay Ctrl S Default project filenames VERGE E amp Use default filenames InbredPanel Y EvaPropertiesPanel Save Project Import Exit create the project folder cf Project Folders and Paths a Click the icon inside the red circle marked fl Oto create a new folder in the standard project folder If you wish you can browse to another location and create the project folder b Write a proper folder name where the text fNew Folder is highlighted c Double click one the new project folder to enter it d Click fOpeno circle 3 The project name and project path is display in the Eval program
57. tation Peer Berg Head of research unit Population Genetics and Embryology E mail Peer Berg Q agrsci dk Faculty of Agricultural Sciences University of Aarhus Department of Genetics and Biotechnology P O Box 50 DK 8830 Tjele Denmark Morten Kargo S rensen Senior Advisor E mail Morten Kargo Q agrsci dk Faculty of Agricultural Sciences University of Aarhus Department of Genetics and Biotechnology P O Box 50 DK 8830 Tjele Denmark Side 3 af 41 Your complimentary use period has ended Thank you for using PDF Complete a Interface User Manual VERSITET fed Features External system Developer Faculty of Agricultural Sciences University of Aarhus Department of Genetics and Biotechnology P O Box 50 DK 8830 Tjele Denmark Motivation Inbreeding reasons and consequences Those involved in animal breeding are familiar with the concept of inbreeding and most are aware of the fact that inbreeding has unfavourable effects The degree of inbreeding is the probability that both genes of a gene pair originate from the same ancestor Inbreeding which thus only can occur if the parents are related has three unfavourable consequences Inbreeding depression Reduction of genetic variance Expression of hereditary defects Balance between genetic gain and additive genetic relationship Inbreeding is a problem in populations that are small in numbers because the animals to a certain
58. terface The changes in Peers Eva program are the following e Genetic merit of candidates given in the input data file are standardised in order for weights to be comparable across datasets e Prediction of rate of inbreeding in output Futures Planned for version 2 0 of Peer Bergs Eva program Basic changes e Computations of average relationships based on Meuwissen amp Sonesson 1998 e EVA will be less memory consuming due to the implementation of the algorithm proposed by Colleau Colleau J J 2002 An indirect approach to the extensive calculation of relationship coefficients Genet Sel Evol 34 409 421 to compute average relationships Parameter changes e Parameter Annual o If false the default average relationship is minimised o If true rate of inbreeding is minimised e Two estimates of rate of inbreeding o 1 based on the age profile of the optimal solution o 2 based on the age profile of the previous generation Contact Peer Berg peer berg agrsci dk Morten Kargo morten kargo agrsci dk Jes Nielsen Side 36 af 41 Your complimentary use period has ended Interface User Manual Thank you for using PDF Complete F TTER fed Features rs nielsen agrsci dk Appendix A Eva and Eva Inbred Documentation Please note that this is a changed and reduced version of Peer Berg EVA UsersG Guide Introduction This document is a guide to the use of the two programs in EV
59. terface ver 1 3 02 Update 1 Example 5 File Run Project Help File Run Project Help EVA EVA Inbr ed EVA EVA Inbred BE ib Custom Diagram erage je mating frequence Aver rage generation n coefficie nt by grou up AL a FE l Custom Diagram gi Average mating frequence f ll Average generation coefficient by group Custom diagam 1940 1945 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 Group 1034 201 DEL nannan coefficients Relation Largest genetic contributions Inbred Parameter file Log file reeding j coefficients Relationships Largest genetic contributions red ships ad eat j Summary og ers Results Run Eva Inbred Project name Example Project path Projects Example Picture to the left shows result table selection and picture too the right shows the new custom diagram Formatting chart diagrams It is possible to change how the charts graphics is presented This is especially Properties valuable when you make you own custom diagram because title and legends do not match the data presented You can change how a chart looks like by right Print clicking on the chart This will activate the right click menu from which a Zoom In gt Zoom Out b number of menu item are available The fProperties Omenu gives you access
60. the below picture Sire Dam N mating Nf EBV F 1 2 1 0 4653 0 00000 0 4 3 4 2 0 1406 0 00000 0 4 3 10 3 0 8520E 01 0 00000 0 5 9 6 0 2506 0 00000 0 4 9 8 5 0 1431 0 00000 0 4 11 12 6 0 1409 0 00000 0 4 11 4002 F 0 3460 0 00000 0 17 14 8 0 1200 0 00000 0 4 17 20 9 0 2449 0 00000 0 5 19 4010 10 0 3101 0 00000 0 The description of each variable is explained in the following table Variable Description Format N Mating Number of mating numbered Integer from 1 to number of matings Mating number for sire Nf m Mating number of dam within Integer sire EBV Estimated Breeding value Coefficient of inbreeding of offspring from mating between sire and dam vF Mendelian sampling variance Real factor for offspring that is mendelian variance is vf Va where Va is genetic variance VF is between 0 and 1 2 Sire Text field with an optional text Characters string from the input file Dam Text field with an optional text Characters string from the input file Mating list Male_list txt Contain a list of males with the number of matings per male and the optional information on males given I in data file as shown in the picture below M matings sire TXT 1 1 trojan Description of Eva Inbred Results Eval Tabname The Eval Tabname actually specify what is printed on the result tabs in the Eva Interface A result tabs is a zZz ENENENENE ES T ft ft ft fot fot ft fot fo f 0o000000000 lt graph
61. tp eva agrsci dk Hvad skal Firefox g re med denne fil C Abn med WinZip Executable standard l G r dette automatisk for filer som denne fremover gt Downloads ST Tel Eval 1 3 02 Update 2 zip bn F rdig Fjern Ryd liste Alle filer gemmes i mappen Ej Skrivebord a Please continue the installation by reading the AlnstallO paragraph below Installing The following series of steps help you install Eval presuming that you either have located the Eval installation on disk or on you CD ROM drive If you do not know where the Eval installation file is located then please read the above installation procedure Overview 1 Start the Windows Explorer 2 Browse to the folder where you save the Eval zip file 3 Double click the Eval Zip file in the right part of the Windows Explorer window 4 Double click the Eval exe file when your unzip program starts 5 Follow the instructions given by the installation program Details 10 OGem p diskOin Danish is ave on diskOin English Side 14 af 41 fed Features Abn Command Prompt Here Sag W Scan for viruses OStifinderd Explorerd Browse to the location of the Eval zip file and double click the zip file This should start your zip program If nothing happens check that your zip program is properly installed Add to archive Add to Menuen Start rar Compress and email
62. with permission and a valid Eva program password The Eva program files are password protected and you will not be able to use the programs without a valid password Click the Download Eval link to download Eval or the How to Install link to view installation procedure Filoverf rsel Xx Vil du abne eller gemme denne fil Bz Navn Eval 1 3 02 Update 2 zip Type Winzip File 15 2 MB Fra eva agrsdi dk iv Sp rg altid f r filer af denne type bnes Selvom filer fra Intemettet kan v re nyttige kan nogle filtyper v re y potentielt skadelige for din computer Hvis du ikke har tillid til kilden skal du ikke bne eller gemme denne fil Hvad er risikoen ET 2x Gemi 2 Skrivebord v O 2 eE Dokumenter ig Denne computer Netveerkssteder help KFC Apps kvikko SCP ED Membership zip NGH EVA Kurser Side 13 af 41 use period has ended p Thank you for using ike mere I using Abner Eval 1 3 02 Update 2 zip a x Firefox you click on ave to diskd and click the Ok button Firefox then downloads the installation file to the default download folder You can find this folder by clicking MFunctionsO and MDownloadsOin the Firefox menu Then a window appears that looks like the next image Where the installation file is save is written in the bottom of this window indicated by a red circle Du har valgt at bne CJ evar 1 3 02 Update 2 zip Hvilket er en et WinZip File fra ht
63. y evident in the living animal The breed was included in the animal subsidy arrangement in 1998 Tips amp tricks The following section contains some tips and tricks to use in EVA Interface You are welcome to send us further tips and tricks if you discover some new tips and tricks that are not here Adding Eva and Inbred parameter files to a project It is possible to add already developed Eva prm Eva inbred_filenames prm and inbred prm files to project created by EVAI There are two possible approaches to doing this I Use EVAI and import prm files into current projects cf below fUse EV AI or 2 Copy the files directly into the project folder cf below MCopy files directly6 Use EVAI 1 Open or create a project Side 34 af 41 Your complimentary use period has ended Interface User Manual L Co m p ete DF Complete VERSITET a d Features enu and choose the file you want to import into current oe Repeat this for all the files you want to add to currently opened project 3 Save project Copy files directly 1 Close EVAI if the program is running Use you favourite file browser and copy the prm files you want to use into one of the project folders 3 Start EVAI and EVAI will pick up the values in the prm files automatically Please note that this approach needs the exact file names to match these Failures and possible solutions I installed as described e Did you ins

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