User Guide
Contents
1. Batch Results Comparison 12 O The first line specifies the program Must match spelling on dropdown list The second line specifies the pathway to the true genotype file The third line specifies the pathway to the program output file The fourth line specifies the number of candidate parent and offspring files which in the case of NEWPAT is always zero The fifth line specifies the pathway and name of the file where results will be saved The sixth line contains a value of either 0 or 1 indicating maternity and paternity analyses respectively See the NEWPAT program section for more details PARENTAGE and PARENTE both require a single file specifying an ID linking file and candidate parent and offspring file respectively and an additional line specifying a probability level for analysis Here is an example for PARENTE Parente True Genotypes Trimmed txt Parentage AssignmentiPARENTE pair txt 1 Parentage Assignment PARENTE appa PAR txt Batch Results Comparison 0 25 The first line specifies the program The second line specifies the pathway to the true genotype file The third line specifies the pathway to the program output file The fourth line specifies the number of candidate parent and offspring files 13 O The fifth line specifies the pathway to the candidate parent and offspring file The sixth line specifies the pathway and name of the file where results will be saved The seventh line spe2. Sheikh and T Y Berger Wolf 2009 KINALYZER a computer program for reconstructing sibling groups Molecular Ecology Resources 9 1127 1131 Butler K C Field C M Herbinger and B R Smith 2004 Accuracy efficiency and robustness of four algorithms allowing full sibship reconstruction from DNA marker data Molecular Ecology 13 1589 1600 Carvajal Rodriguez A 2007 FAMSPHERE a computer program for parental allocation from known genotypic pools Molecular Ecology Notes 7 213 216 Cercueil A E Bellemain and S Manel 2002 PARENTE Computer program for parentage analysis Journal of Heredity 93 458 459 Coombs J A B H Letcher and K H Nislow 2008 CREATE a software to create input files from diploid genotypic data for 52 genetic software programs Molecular Ecology Resources 8 578 580 Coombs J A B H Letcher and K H Nislow 2010a PEDAGOG Software for simulating eco evolutionary population dynamics Molecular Ecology Resources in press Coombs J A B H Letcher and K H Nislow 2010b PedAgree Software to quantify error and assess accuracy and congruence for genetically reconstructed pedigree relationships Conservation Genetics Resources in press Danzmann R G 1997 PROBMAX A computer program for assigning unknown parentage in pedigree analysis from known genotypic pools of parents and progeny Journal of Heredity 88 333 Duchesne P T Castric and L Bernatchez 2005 PASOS parental allocation of si
3. assigned parent 10989 because parent 10629 had a proportion of 0 2051 which is below the minimum threshold value Individual ID Parent 1 Parent 2 11837 11136 10080 11838 11136 10080 11921 11136 10080 12084 10931 11272 12040 10931 11272 12125 10989 0 12149 10989 0 A table showing the number of parentage assignments required to be accepted as parent for entire family based on family size and minimum threshold value is shown below 43 O Threshold values Family Size 0 1 0 1 0 15 0 2 0 25 03 035 04 0 45 0 5 OO OND OBR W P _ Output file three is a pedigree file containing individuals and their assigned parents The pedigree is created by the sibship constraint method using a minimum full sib family size of one and a minimum threshold value equal to zero The format of the file is three columns with each row containing the offspring identifier followed by the identifiers of its assigned parents Output files four five and six produce differing versions of the pedigree file dependent upon the minimum full sibling size specified All three output files are formatted identical to file three as described above with an individual s identifier followed by the identifiers of its two assigned parents Output file four contains pedigree information for all individuals but only uses parents constrained by sibship for individuals belonging to full sibling groups greater than or equal to the user specified value
4. the reference for the program and a website from which the program can be downloaded are specified Cervus Overview 21 CERVUS uses genetic data from unlinked co dominant genetic markers such as microsatellites STRs single nucleotide polymorphisms SNP s and allozymes it performs allele frequency analysis parentage analysis simulations and parentage analysis Additional Requirements Be sure to specify the program output file with the csv extension and not the text file with the same name In order to make the comparison PedAgree requires that all of the candidate parent and offspring files used to create the CERVUS output file be specified in the Candidate Parent and Offspring File s area When running a CERVUS comparison you will be prompted by the below form for a level of confidence at which to conduct the analysis Cervus Confidence Level E Oo Please select a trio confidence level at which to assess the output C Strict Confidence Assigned Parent C Most Likely Non Assigned Parent C All assignments Select The strict and relaxed confidence levels are used as a means of designating assigned parents where the probability is above those levels when derived from the simulations The default values for strict and relaxed are 95 and 80 22 O respectively but any values are able to be specified during the analysis in CERVUS The most likely non assigned
5. 0 means that neither assigned parent from output 1 equals either assigned parent from output 2 Below is an excerpt from a Reconstructed True parentage assignment details file The program correctly assigned both parents for offspring 11695 The program incorrectly assigned both parents for offspring 11719 Since both or the parents were sampled the relatedness of the incorrectly assigned individuals is given Parent 1 was a half sibling to the dam while parent 2 was not a sibling of the sire For offspring 11722 the program correctly identified the sire while incorrectly assigning the full sibling to the dam Parent 1 was not assigned for offspring 11753 even though the dam was sampled Therefore a relatedness of Not Assigned is given For offspring 10711 parent 1 was incorrectly assigned given that the true parent was not sampled Parent 2 was correctly unassigned given that the sire was not sampled For offspring 10726 both parents were correctly unassigned given that both the dam and sire were not sampled Offspring Dam Assigned Sire Assigned Parent 1 Assignment Parent 2 Assignment Score Misassigned Misassigned Parent 1 Parent 2 Description Description Parent 1 Parent 2 Relatedness Relatedness 11695 11172 11172 10327 10327 Right Sampled Right Sampled 2 11719 11172 10961 10327 11087 Wrong Sampled Wrong Sampled 0 Half Sib Non Sib 11722 11172 11159 10327 10327 Wrong Sampled Right Sampled 1 Full Sib 11753 10699 0 10285 10285 Wrong Samp
6. For individuals belonging to groups smaller than the threshold size the assigned parents are taken from the parentage assignment output file The output file has a Pedigree Min FS Size of 5 Complete txt extension where 5 changes to equal the user specified value Output file five reports an incomplete pedigree containing only individuals belonging to a full sibling group greater than or equal to the specified threshold Thus all individuals in this file have parents assigned using sibship constraint This file has a Pedigree Min FS Size of 5 Incomplete txt extension where 5 changes to equal the user specified value 44 O Output file six also reports an incomplete pedigree containing only individuals belonging to a full sibling group greater than or equal to the specified threshold The difference with this file is that it reports the parents from the source parentage assignment output file thus allowing for direct comparison to the incomplete constrained file for accuracy assessment and congruence Output file six has a Pedigree Min FS Size of 5 Incomplete txt extension preceded by the name of the parentage assignment program and where 5 changes to equal the user specified value Example Data Included with the software are a true genotype file program input and output files for all of the sibship reconstruction and parentage assignment programs ID linking files and candidate parent and offspring f
7. LOD Scores menu Once the analysis has been run save the output to a text file 24 O In order to make the comparison PedAgree requires an ID linking file Reference Gerber et al 2003 Download http www pierroton inra fr genetics labo Software Famoz famozinstall famozinst all_ct html Famsphere Overview FAMSPHERE implements a distance based method to allocate families based on microsatellite marker information It formalizes the exclusion method considering genotyping errors or mutations Contrary to the standard exclusion method FAMSPHERE provides a way to resolve conflicts in the case of multiple paternities The information linked to the defined distances is similar to that of the transmission probabilities used in the likelinood approaches However in FAMSPHERE the information of loci is used as a whole contrary to the likelinood approaches Additional Requirements Select the file fam out for the program output file In order to make the comparison PedAgree requires that both of the candidate parent and offspring files used to create the FAMSPHERE output file be specified in the Candidate Parent and Offspring File s area Reference Carvajal Rodriguez 2007 25 O http webs uvigo es acraaj famsphere htm Download Gimlet Overview GIMLET estimates error rates during genotyping and constructing consensus genotypes from repeated genotyping pools identical genotypes among a set of severa
8. assigned individuals is equal to the total number of individuals minus the minimum number of individuals that must be moved to convert assigned family structure to true family structure 6 Accuracy of families greater than or equal to a specific family size and reported for values of 2 3 4 5 and 10 This last section is not a measure of true accuracy in that it only assesses whether individuals assigned to a full sib family are indeed full sibs It does not take into account splitting of larger true full sib families For example if a true full sib family of size ten were assigned to two full sib families each of size five they would still be correct in that all members within each assigned family are indeed full sibs This error would instead show up in the total accuracy mentioned above Below is an example of a sibship reconstruction summary output file There were nine assigned full sib families compared to ten true full sib families The score for this comparison is 16 20 or 0 8000 This means that four individuals were assigned to the wrong family 34 O Number of Full Sib Families True Assigned 10 9 True Full Sib Families Family Size SANDS ed epee Assigned Full Sib Families Family Size 4 CeO IS eve ny nNwww Member ID s 5034 5037 5040 5044 5046 5061 5063 5065 5082 5083 5085 5117 5123 5130 5139 5051 5078 5088 5108 5124 Member ID s 5051 5082 5083 5085 5061 5063 5065 5034 5
9. file The third line specifies the pathway to the program output file The fourth line specifies the pathway and name of the file where results will be saved Format 2 The second form consists of five lines and is used for the following programs that require an ID linking file COLONY_V1 PRT FAMOZ and PEDAPP 11 O Here is an example Colony_V1 True Genotypes Trimmed txt Sibship Reconstruction COLONY V1 output colony txt Sibship Reconstruction COLONY V1 COLONY ID TABLE txt Batch Results Comparison The first line specifies the program Must match spelling on dropdown list The second line specifies the pathway to the true genotype file The third line specifies the pathway to the program output file The fourth line specifies the pathway to the ID linking file The fifth line specifies the pathway and name of the file where results will be saved Format 3 The last form consists of at least six lines and is used for the following programs that require an ID linking file or a candidate parent and offspring file or files and or a probability or level of analysis PARENTAGE CERVUS FAMSPHERE NEWPAT PASOS and PARENTE NEWPAT does not require a linking or candidate parent and offspring file but does require a value specifying whether the analysis is will be for maternity or paternity Here is an example for NEWPAT Newpat True Genotypes Trimmed txt Parentage Assignment NEWPAT RESULTS TXT 0
10. parent 1 and dam identifiers and the assigned parent 2 and sire identifiers There are four possible descriptions for a comparison 1 Right Sampled means that the true parent was sampled or present in the program input file and the assigned parent equals the true parent 2 Right Not Sampled means that the true parent was not sampled and no individual was assigned by the program 3 Wrong Sampled means that the true parent was sampled but the program either assigned the wrong individual or no individual at all 4 Wrong Not Sampled means that the true parent was not sampled but the program assigned an incorrect individual Score provides the number of correct comparisons for the individual A score of two means that both assigned parents equal their associated true parent A score of 1 means that one of the assigned parents equals one of the true parents while the other assigned parent is incorrect A score of O means that neither assigned parent equals either true parent 36 O The misassigned parent 1 and 2 relatedness columns specify the relatedness between the incorrectly assigned parent and the true parent if the true parent was sampled The relatedness description can be one of four things 1 Full Sib means that the assigned parent shared both of its parents with the true parent 2 Half Sib means that the assigned parent shared one of its parents with the true parent 3 Non Sib means that the assigned parent did not share either of it
11. sub samples offspring OFS candidate males CMS and candidate females CFS Individuals in OFS are assigned clustered to K1 paternal and K2 maternal families K1 and K2 unknown individuals in CMS and CFS are assigned paternity and maternity to these K1 and K2 families It is assumed that offspring are either full sibs sharing both parents half sibs sharing only one of the two parents or unrelated sharing no parents while candidates are unrelated and are either parents of or unrelated to the offspring Markers are assumed to be in linkage equilibrium and Hardy Weinberg equilibrium Violation of these assumptions may lower the power of the analysis but could be compensated by using more informative markers Wang 2004 For example the information about the sex and age of the sampled individuals might be unavailable In such a case each individual is allowed to appear in all 3 sub samples and the sibship and parentage are still inferred satisfactorily in some cases Additional Requirements For sibship analysis select the file with the extension BestFSFamily extension Reference Wang amp Santure 2009 Download http www zsl org science research software colony 1154 AR html Kingroup Overview 17 KINGROUP s main objective is to test hypotheses of pedigree relationships between pairs of individuals using data from codominant single locus genetic markers Additional Requirements After the analys
12. 044 5046 5037 5117 5123 5078 5108 5130 5139 5088 5040 5124 True Family Size 1 5 Se N SaasSenes SSSSSREGS Total 16 20 0 8000 Assigned Family in True Family Size 3 3 3 4 1 3 1 1 3 3 3 4 2 3 2 2 1 4 1 2 1 1 1 2 1 1 00 AO 04 n0 Accuracy for assigned full sib families of size gt 10 0 0 0 0000 Accuracy for assigned full sib families of size gt 5 0 0 0 0000 Accuracy for assigned full sib families of size gt 4 3 4 0 7500 Accuracy for assigned full sib families of size gt 3 11 13 0 8462 35 O Parentage Assignment Output Files Accuracy for assigned full sib families of size gt 2 14 17 0 8235 A parentage assignment comparison for either the Reconstructed True or the Reconstructed Reconstructed Comparison results in the creation of two output files The first one is a detailed file that lists the following information for each individual Reconstructed True Comparison Individual identifier dam identifier assigned parent 1 sire identifier assigned parent 2 parent 1 assignment description parent 2 assignment description score misassigned parent 1 relatedness and misassigned parent 2 relatedness The dam and sire identifiers come from the true pedigree file The assigned parent 1 and assigned parent 2 identifiers come from the program output file The parent 1 and 2 assignment descriptions describe the comparison between the assigned
13. 4 Download http herbinger biology dal ca 5080 Pedigree Overview Pedigree Reconstruction Tools PRT is specifically designed for a single generation of organisms without parents present The input is a table of DNA 20 O markers and the output is a partition of the organisms into putative sibling groups Additional Requirements Before running the analysis in PRT select and delete all data in the output window Run the analysis in PRT Once PRT has finished running click on the File menu and select Save output Select this file for the program output file in PedAgree In order to make the comparison PedAgree requires an ID linking file Reference Almudevar amp Field 1999 Download http www urmc rochester edu biostat people faculty almudevar cfm Parentage Assignment Programs PedAgree currently makes comparisons for thirteen parentage assignment programs All thirteen programs require the presence of a true pedigree file and an output file generated by the selected program Additionally some of the programs require an ID linking file to relate the generic identifiers used by the program to the actual identifiers used in the true pedigree file or a candidate parent and offspring file or files to account for the availability of potential parents For each of the thirteen programs a general overview of what the program does additional requirements needed for PedAgree to make the comparison
14. A Copy the output control C and paste control V it into a new notepad file and save it as your output file Reference Hedgecock amp Eichert 1999 Download http www bml ucdavis edu whichparents html PedAgree Overview PedAgree is a program for comparing reconstructed pedigree files to true known pedigrees or other reconstructed pedigrees Additionally if a sibship reconstruction output file is compared to a parentage reconstruction output file the two proportionately highest assigned parents for each full sibling group defined by the sibship reconstruction output file will be tabulated A pedigree file will be generated using these parents as the parents for all members of each full sib family that exceed a user defined threshold Additional Requirements None Reference Coombs et al 2010b Download 32 O https bcrc bio umass edu pedigreesoftware Sibship Reconstruction Output Files A sibship reconstruction comparison for either the Reconstructed True or the Reconstructed Reconstructed Comparison results in the creation of two output files The first one is a detailed file listing the following information for each individual Individual identifier true full sib family number true full sib family size assigned full sib family number and assigned full sib family size Below is an example of a sibship reconstruction details file There are six true full sib families and seven assigned fu
15. ASOS do not require the eighth line If there was an error encountered during the run you will see the following popup upon completion Pedagoggles Comparison Complete Please check the Error Log txt file The Error Log txt file will be located in the same folder as the selected batch file Upon opening the file you will see a line for each error encountered Below is an example of the contents found in an error log file 2 CERVUS Could not find true pedigree file 3 PARENTE Could not find ID linking parent offspring input file The first column refers to the ordered numerical location of the comparison generating the error In the example both the second and third comparisons in the batch file generated errors The second column refers to the selected program of the comparison generating the error In the example the programs of the error generating comparisons are CERVUS and PARENTE The third column explains what generated the error In the example the CERVUS comparison could not locate the true pedigree file while the PARENTE comparison could not locate the parent offspring input file Sibship Reconstruction Programs PedAgree currently makes comparisons for seven sibship reconstruction programs All seven programs require the presence of a true pedigree file and an output file 15 generated by the selected program Additionally some of the programs require an ID linking file to relate the generic iden
16. Assignment proportions for instances where an assignment was made 157 266 0 5902 Sampled and Incorrectly Assigned 40 266 0 1504 69 266 0 2594 Sampled and Correctly Assigned Unsampled and Incorrectly Assigned Reconstructed Reconstructed 1 If the program producing the output was CERVUS PARENTE or NEWPAT there will be a line stating the level probability or type of analysis under which the comparison was conducted 2 The ratio and proportion of congruence between assigned parents from the two outputs 3 The ratio and proportion of congruence between assigned parents for varying categories where one or both parents were assigned in one or both outputs Sibship Parentage Comparison 40 O A sibship parentage reconstruction comparison for the Reconstructed Reconstructed Comparison option requires user input for two variables and results in the creation of six output files The first variable requiring user input is the Minimum Full Sibling Size shown below This value determines the minimum family size for which to constrain parentage see below Minimum Full Sibling Size 5 Enter the minimum full sibling size with which you wish to constrain parentage if The second variable requiring user input is the Minimum Threshold Value shown below This value determines which parents to use for sibship constraint see below Minimum Threshold Value 5 Enter the minimum proportion of full
17. Errors can arise when any of the following occur 1 an incorrect individual was assigned when the true parent was sampled 2 no individual was assigned when the true parent was sampled or 3 an incorrect individual was assigned when the true parent was not sampled Errors are broken down into situations where neither true parent was sampled one true parent was sampled while one was not or both true parents were sampled For cases where an incorrect parent was assigned when the true parent was sampled the error is further broken down by classifying the relationship between the two as either full sib half sib or unrelated Finally accuracy is assessed for instances where both parents were assigned regardless of whether the true parents were sampled or not Citation To cite PedAgree please use the following Coombs J A Letcher B H and Nislow K H 2008 PedAgree Software to quantify error and assess accuracy and congruence for genetically reconstructed pedigree relationships Conservation Genetics Resources n press Installation O A zip file containing the program PedAgree a user guide and example data files is freely available for download from https bcrc bio umass edu pedigreesoftware The program is a stand alone executable version that is fully operational once unzipped Example files are included to provide data for experimentation with PedAgree in order for the user to gain familiarity Getting Started To start
18. Ped gt Updated February 4th 2010 r User Guide Jason A Coombs Benjamin H Letcher Keith H Nislow Program In Organismic and Evolutionary Biology University of Massachusetts Amherst MA 01003 jcoombs cns umass edu S O Conte Anadromous Fish Research Center US Geological Survey Leetown Science Center Turners Falls MA 01376 USA Northern Research Station US Forest Service University of Massachusetts Amherst MA 01003 USA O Table of Contents a 6 13 22525228 cecececete cere a aa a a B a Beate eeteweeas 3 A tesserae ate E ceneu A R E 4 Installati n sna sekacie its is iaa aisla weds areas ia 4 G tting Started pres al ts bd les 5 Baten File FOMNals 2cakenebawekaseteoeeed anna E EE E ps ai ae e ad ae 10 Sibship Reconstruction Programs 0 000 cee ees 15 COGN V2 cet ecto oe ee eee Renee 8 Pe iia 16 Colony V2 0 dat e eG eee 16 ANO ecards 17 2 gr vea PAN eestor eeeeeeeeesenseee eee A ia ub ee 18 Parentage A dene edeGincnbeudinn SESee OR GES Sade wee Rs 19 Pedigree te Meee peewee Vera eee a Ea aiina Eana ve rees eee 20 PR ienee ETA 20 Parentage Assignment Programs s aasan anaana 21 CENUS eee a ere E E NS 21 Colony V2 0 ounit i erre eet bebe E BANE 23 FAMOZ sa ao adi a aia iai a a a a ia veh di A A e a a ume gad 24 PomMspnelrea coodaacd eke O 25 A Acie tints A A Peo hed ete aes 26 A te cue eeeeheheksacanectween RESER 26 ct ee ee er ee ee ee ee ee 27 A RC ee eee oes eeten ae 28 PASO
19. S oema ieee Goh ooh cote AAA te eee sees 30 POOR cee hee eco desk oe eons a a eee E 30 o ccossscne cite srehebshessarauese sa necegadedeeeece aes sae sy 31 WhichParents o 02 lt 0 200008 2tid0ntubt Enbbdeedbemahortadsetidda aoe 31 A AO 32 Sibship Reconstruction OUtpUt ocooccccocoooccc 33 Parentage Assignment Output scese desea ara o a aaa daa eds 36 Sibship Parentage Reconstructed Reconstructed Comparison 40 Example Dala ae caie e a ek a aa ainia 45 Disclaimer and Feedback oooooooororrn teen eeeeeeeeeees 45 A E 46 Introduction PedAgree is a program for the rapid comparison of reconstructed relationships against a known pedigree for evaluative purposes and for comparison of reconstructed relationships against one another to assess congruence of differing algorithms Specifically it was designed as a companion program to the simulation software PEDAGOG Coombs ef al 2010a to evaluate existing sibship reconstruction and parentage assignment programs Theoretically PedAgree could be used with any dataset for which there is a known pedigree The advantage of using it with PEDAGOG is that PEDAGOG allows the user to vary numerous parameters such as mating strategy mate choice fecundity cohort size capture probability survival migration rates age error sex error known parent error genotype error mutation linkage and genotype scoring probability to name a few All of these parameters are then outp
20. amily were assigned the same parent than the proportion for each parent would be 0 5 COLONY Family CERVUS Parent 1 Proportion CERVUS Parent 2 Proportion 1 11136 0 3774 10080 0 2736 2 10931 0 4135 11272 0 2981 3 10989 0 3718 10629 0 2051 42 O Files three four and five contain pedigree output that uses the sibship constraint method to improve accuracy of assigned parents This method uses full sibling family composition from the sibship reconstruction output file to assess parentage assignment agreement The method records the proportion of assignments for each candidate within a full sib family out of the total number of possible assignments The two candidates with the highest assignment proportions are then compared to the Minimum Threshold Value and if greater than or equal to that value are assigned to all members of the full sib family otherwise an assignment of 0 is given An example is shown below that corresponds to the data shown for the summary output file above and used a minimum full sib family size equal to 2 and a minimum threshold value equal to 0 2501 Individuals 11837 11838 and 11921 were from full sib family 1 and thus were assigned parents 11136 and 10080 because both of their proportions were greater than 0 2501 Likewise individuals 12084 and 12040 were from family 2 and thus were assigned parents 10931 and 11272 However 12125 and 12149 were only
21. ch file a value should be entered on the fourth line This value should equal 0 if a maternity analysis is being conducted or 1 if a paternity analysis is being conducted Reference Wilmer et al 1999 Download http Awww zoo cam ac uk zoostaff amos newpat htm Overview PAPA is a parental pair allocation and simulator program The allocation method is based on the likelihood of a parental pair producing the multilocus genotype found in the offspring being tested which will be referred to as the breeding 27 O likelinood Estimated level and structure of allele transmission errors in offspring are parameters fed into the allocation procedure The embodied Monte Carlo simulator also allows modeling of many allocation conditions including transmission error and the estimated proportion of missing parents Simulations may be run prior to the collection of real parents in order to define the minimal set of loci that is necessary to reach a desired level of allocation success Post collection simulations aim at statistically assessing the reliability of non simulated allocations Simulations output values for several random variables Additional Requirements Be sure to select the allocation results xls output file and not the text file of the same name as the program output file Reference Duchesne et al 2002 Download http www2 bio ulaval ca louisbernatchez downloads htm Parente Overview PARENTE uses genoty
22. ch the comparison was conducted If the program producing the parentage output was CERVUS PARENTE or NEWPAT there will be a line stating the level probability or type of analysis under which the comparison was conducted 2 The number of full sib families for the sibship output and the parentage output The sibship family structure is obtained directly from the sibship output file The parentage family structure is created from the parentage output file and is based on the sharing of parents assigned to individuals 3 The number size and composition of each sibship and parentage full sib family 4 The number and proportion of parentage full sib families required to account for the composition of each sibship full sib family 5 The score reported as the ratio and proportion of individuals assigned to parentage full sib families agreeing with sibship full sib family assignments 6 The parent pair accounting for the highest proportions of assigned parents for individuals composing sibship full sib families Parts 1 through 5 are identical in appearance to the sibship summary file described above in the sibship reconstruction output files An example of part 6 is shown below This file shows that sibship families were acquired from COLONY and parentage was acquired from CERVUS For family 1 parents 11136 and 10080 accounted for 0 3774 and 0 2736 of individual parent assignments respectively If all individuals in a full sib f
23. cifies the assigned parent probability for which to conduct the comparison analysis See the PARENTAGE or PARENTE program section for more details CERVUS FAMSPHERE and PASOS require the candidate offspring file and the candidate parents file if sex is known then both the candidate mothers and candidate fathers files must be specified for CERVUS and PASOS CERVUS requires an additional line containing an integer between 0 and 4 specifying the analysis level Here is an example for CERVUS Cervus True Genotypes Trimmed txt Parentage Assignment CERVUS output cervus csv 2 Parentage Assignment CERVUS CERVUS OFFSPRING txt Parentage Assignment CERVUS CERVUS PARENTS txt Batch Results Comparison 3 The first line specifies the program Must match spelling on dropdown list The second line specifies the pathway to the true genotype file The third line specifies the pathway to the program output file The fourth line specifies the number of candidate parent and offspring files The fifth line specifies the pathway to the first candidate parent and offspring file The sixth line specifies the pathway to the second candidate parent and offspring file The seventh line specifies the pathway and name of the file where results will be saved 14 The eighth line specifies the assigned parent confidence level for which to conduct the comparison analysis See the CERVUS program section for more details FAMSPHERE and P
24. iles both detail and summary comparison PedAgree output files and a batch file set to run all of the example files Additionally there is a file titled Apparent Genotypes txt This file can be used with the program CREATE Coombs et al 2008 to make new input files for the sibship reconstruction and parentage assignment programs These files are provided to give the user examples of file formats output data and for experimentation with PedAgree Disclaimer and Feedback This program is provided as is Authors and providers are not responsible in case of errors You may distribute this program freely in any format so long as the following conditions are met The program remains intact without modification the user guide is included without modification and no fee of any kind is charged If there are additional programs that you would like to have added to PedAgree please let us know If you encounter any problems with PedAgree please let us know as well We will attempt to promptly track down and fix any bugs that are reported 45 References Almudevar A 2007 A graphical approach to relatedness inference Theoretical Population Biology 71 213 229 Almudevar A and C Field 1999 Estimation of single generation sibling relationships based on DNA markers Journal of Agricultural Biological and Environmental Statistics 4 136 165 Ashley M V I C Caballero W Chaovalitwongse B Dasgupta P Govindan S I
25. ing file associated with the program selected in step 1 Not all programs require this input If the selected program does not require it then this region will be disabled and a selection will be unable to be made Several of the programs require the input of an ID linking file which links the generic identifier used by the program to the actual identifier used in the true pedigree file This file must contain two columns of information separated by a tab The two columns contain the identifier found in the true pedigree file and the generic identifier used by the sibship reconstruction or parentage assignment program Four programs CERVUS FAMSPHERE PASOS and PARENTE require the selection of the input file or files used by the selected program in order to account for which individuals were available for assignment Simply select the drive and folder housing the file s and then highlight the file s in the file listbox To select multiple files press and hold the control key while clicking on the file name with the mouse The button displaying the lt character changes the current folder to the folder selected in the program output directory The button displaying the character moves the current folder up one level The results folder text box holds the pathway to the folder where you want the results to be output The results filename textbox holds the name of what you wish to call the results file You do not need to add an extension
26. ion of a new folder The new folder will be created in the folder currently selected The command button labeled Cancel closes the form without changing the pathway in the results folder text box The command button labeled Select closes the form and changes the pathway in the results folder text box to that selected in the form 10 The command button labeled Compare runs the algorithm of the program that does the comparison of the specified files for all three options When the program is finished it will present the following pop up Pedagoggles Comparison Complete If you were running a batch file and there was an error encountered then you will receive the following popup Pedagoggles Comparison Complete Please check the Error Log txt file This indicates that at least one of the comparisons specified in the batch file was unable to be run Check the Error Log txt file to determine which comparison generated the error This file will be created in the same folder in which the batch file was located Batch File Format Batch files are a way to run multiple sibship reconstruction and or parentage assignment output comparisons using a single file The format of the batch file input specifications can take one of three forms depending on which sibship reconstruction parentage assignment program is being specified There are explanations and examples of the three forms given bel
27. is has run in KINGROUP click anywhere on the results table and select all the output control A Copy the output control C and paste control V it into a new notepad file and save it as your output file Reference Konovalov et al 2004 Download http code google com p kingroup Kinalyzer Overview Kinalyzer is a software suite developed to reconstruct sibling groups using genotypes from codominant markers such as microsatellites Currently there are two algorithms available to reconstruct full sibling groups for cases where parental genotypes are not available Kinalyzer uses combinatorial optimization based on Mendelian inheritance rules to find the fewest number of sibling groups that contain all the individuals in the sample 2 allele set cover Also available is a consensus method that reconstructs sibgroups using subsets of loci and finds the consensus of these different solutions Additional Requirements None Reference Ashley et al 2009 18 Download http kinalyzer cs uic edu Parentage Overview PARENTAGE was developed to draw inferences for the problem of shared maternity with an unknown number of fathers and no additional information except for allele frequencies in the breeding population Additional Requirements Select the output file that has the paternity extension In order to make the comparison PedAgree requires an ID linking file When running a PARENTAGE compar
28. ison in PedAgree you will be prompted by the below form for a probability at which to determine if individuals share a same parent Probability Cutoff Please enter the probability cutoff determining if individuals share the same parent lt This value must be greater than or equal to 0 and less then or equal to 1 If specifying a PARENTAGE comparison in a batch file the probability value is entered on the seventh line Reference 19 O Emery et al 2001 Download http www staff ncl ac uk i j wilson Pedigree PRT Overview The primary objective of PEDIGREE is to reconstruct the full pedigree in a group of individuals based on their genotype data with the complete absence of parental information The program allows the user to potentially reconstruct the set of single generation relationships among individuals i e which individuals are most likely full sibs half sibs and unrelated In addition it allows generating the genotype of the unknown parents Additional Requirements Once the run has completed go to the View Details link under the Commands column heading For whichever run you wish to analyze click on the Groups link under the View column heading Click anywhere on the page and select all the output control A Copy the output control C and paste control V it into a new notepad file and save it as your output file Reference Smith et al 2001 Butler et al 200
29. k and J M Pemberton 1998 Statistical confidence for likelinood based paternity inference in natural populations Molecular Ecology 7 639 655 Smith B R C M Herbinger and H R Merry 2001 Accurate partition of individuals into full sib families from genetic data without parental information Genetics 158 1329 1338 Valiere N 2002 GIMLET a computer program for analysing genetic individual identification data Molecular Ecology Notes 2 377 379 Wang J and A W Santure 2009 Parentage and Sibship Inference From Multilocus Genotype Data Under Polygamy Genetics 181 1579 1594 Wang y L 2004 Sibship reconstruction from genetic data with typing errors Genetics 166 1963 1979 Wilmer J W P J Allen P P Pomeroy S D Twiss and W Amos 1999 Where have all the fathers gone An extensive microsatellite analysis of paternity in the grey seal Halichoerus grypus Molecular Ecology 8 1417 1429 47
30. l genotypes identifies one or several genotype s comparing it them with references determines kinship between individuals and estimates several parameters allelic frequencies heterozygosity probability of identity population size from genotyped samples Additional Requirements Make sure to run the Kinship option under the Identification menu in GIMLET Specify the pair option before running Once the run has completed select the file with the 2P txt extension for the program output file Reference Valiere 2002 Download http pbil univ lyon1 fr software Gimlet gimlet 20frame1 html Newpat Overview NEWPAT is a generalized paternity program which calculates allele frequencies checks for the presence of non amplifying alleles assays each input file for duplicate entries searches for parent offspring relationships according to user inputted criteria and then uses a randomization approach to assess the significance of any matches found 26 Papa Additional Requirements Select the RESULTS TXT for the program output file When running a NEWPAT comparison in PedAgree you will be prompted by the below form to determine if you are conducting a maternity or paternity analysis S Assignment Type E Please select the type of parental analysis you conducted C Maternity searching for mother Paternity searching for father If specifying a NEWPAT comparison in a bat
31. lated and are either parents of or unrelated to the offspring Markers are 23 assumed to be in linkage equilibrium and Hardy Weinberg equilibrium Violation of these assumptions may lower the power of the analysis but could be compensated by using more informative markers Wang 2004 For example the information about the sex and age of the sampled individuals might be unavailable In such a case each individual is allowed to appear in all 3 sub samples and the sibship and parentage are still inferred satisfactorily in some cases Additional Requirements For parentage analysis select the file with the extension BestConfig extension Reference Wang amp Santure 2009 Download http www zsl org science research software colony 1154 AR html Famoz Overview FAMOZ is used in reconstructing parentage for dominant codominant and uniparentally inherited markers Parameters and assumptions used in the calculations are few and simple Exclusion and identity probabilities log likelihoods of any genetic relationship potential father and parent or parent pair half and full sibship are calculated based on real or simulated data Error rates for genotypic mistyping can be introduced Simulations can be done to build statistical tests for parentage assignment Additional Requirements Before running parentage analysis in FAMOZ clear the output window Run the analysis using the Best Parents Couples option under the
32. led Right Sampled 1 Not Assigned 10711 10106 10360 9366 0 Wrong Not Sampled Right Not Sampled 1 10726 10106 0 9366 0 Right Not Sampled Right Not Sampled 2 The second parentage assignment output file is a summary file and contains the following Reconstructed True 1 If the program producing the output was CERVUS PARENTE or NEWPAT there will be a line stating the level probability or type of analysis for which the comparison was conducted 2 The ratio and proportion of correctly assigned parents for the following three situations A Both parents were absent or not sampled 38 B One parent was sampled while the other parent was not sampled C Both parents were sampled Below the three situations is a Summary line giving the ratio and proportion of correctly assigned parents 3 The ratio and proportion of the relatedness categories for situations where the true parent was sampled but not assigned The relatedness categories are further broken down for the scenarios where only one of the true parents was sampled or where both of the true parents were sampled 4 The ratio and proportion of correctly assigned parents for all instances for which a parent was assigned even though the true parent may not have been sampled 5 The ratio and proportion of correctly assigned parents for instances where both parents of an offspring were assigned even though one or both of the true parents may not have been sampled 6 The ratio and p
33. ll sib families The extra assigned family arose from the splitting of true full sib family 1 Individual 11479 belongs to true full sib family 1 which is composed of 22 individuals but was assigned to full sib family 2 which contains 11 members 11479 11481 11487 11488 11489 11490 11491 11493 11497 11504 11507 11508 11514 11520 11524 11482 11485 11498 11501 11502 11503 11516 11476 True Full Sib Family True Full Sib Family Size oO a 2 2 2 A OwWONDDND a a a oe ow oa on on a 22 22 22 22 22 22 Assigned Full Sib Family N A N N NY NH AN FW WO fF BH DY LD Assigned Full Sib Family Size 11 11 11 11 11 11 11 11 11 11 33 11483 1 22 1 11 11511 2 3 3 3 11517 3 3 4 gt 11523 5 2 6 2 11526 4 2 5 2 11477 1 22 2 11 11494 1 22 2 11 11495 1 22 1 11 11505 1 22 2 11 11522 5 2 6 2 The second file is a summary file and contains the following 1 If the program producing the sibship output was PARENTAGE there will be a line stating the probability level at which the comparison was conducted 2 The true and assigned number of full sib families 3 The number size and composition of each true and assigned full sib family 4 The number and proportion of assigned full sib families required to account for the composition of each true full sib family 5 The score reported as the ratio and proportion of correctly assigned individuals out of total individuals where correctly
34. monstrated by applying the minimum description length principle This technique is used in model selection to provide a rational way of comparing models of varying complexity The resulting score may be interpreted and applied as a Bayesian posterior density Additional Requirements 30 O Be sure to select the file containing the com extension for the program output file In order to make the comparison PedAgree requires an ID linking file Reference Almudevar 2007 Download http www urmc rochester edu biostat people faculty almudevar cfm Probmax Overview PROBMAX calculates the maximum probability of progeny assignments to a mixture of possible contributing parents when the genotypes of the parents are known and correspond to the genotypes screened in the progeny and the parental mating combinations are known or potentially known Additional Requirements Be sure to select the file containing the max extension for the program output file Reference Danzmann 1997 Download http www uoguelph ca rdanzman software PROBMAX WhichParents Overview 31 O WHICHPARENTS is a program for determining the most likely parents of offspring using multilocus genotype data If parental mating history is known this program also makes use of that information Additional Requirements After the analysis has run in WHICHPARENTS click anywhere in the report window and select all the output control
35. ngles in open systems a computer program for individual parental allocation with missing parents Molecular Ecology Notes 5 701 704 Duchesne P M H Godbout and L Bernatchez 2002 PAPA package for the analysis of parental allocation a computer program for simulated and real parental allocation Molecular Ecology Notes 2 191 193 46 O Emery A M I J Wilson S Craig P R Boyle and L R Noble 2001 Assignment of paternity groups without access to parental genotypes multiple mating and developmental plasticity in squid Molecular Ecology 10 1265 1278 Gerber S P Chabrier and A Kremer 2003 FAMOZ a software for parentage analysis using dominant codominant and uniparentally inherited markers Molecular Ecology Notes 3 479 481 Hedgecock D Eichert W WHICHPARENTS version 1 0 A windows application for determining the most likely parents of offspring using multilocus genotype data 1999 Computer software distributed from http Awww bml ucdavis edu whichparents html Kalinowski S T M L Taper and T C Marshall 2007 Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment Molecular Ecology 16 1099 1106 Konovalov D A C Manning and M T Henshaw 2004 KINGROUP a program for pedigree relationship reconstruction and kin group assignments using genetic markers Molecular Ecology Notes 4 779 782 Marshall T C J Slate L E B Kruu
36. ontain other information in columns located to the right of these three columns but this information will not be used by PedAgree Simply select the drive and folder housing the file then highlight the file in the file listbox The button displaying the character moves the current folder up one level The checkbox underneath the file selection allows the user to specify whether or not the first line of the true pedigree file contains column headings If the Reconstructed Reconstructed Comparison output option is selected then this region of the form becomes disabled since there is no need for a true pedigree file If the Batch File option is selected then this region of the form specifies the location of the batch file Simply select the drive and folder housing the file then highlight the file itself in the file listbox The button displaying the character moves the current folder up one level This region of the form specifies the location of the output file produced by the program selected in step 1 Simply select the drive and folder housing the file then highlight the file itself in the file listbox The button displaying the lt character changes the current folder to the folder selected in the true pedigree O directory The button displaying the character moves the current folder up one level This region of the form specifies the location of the Identifier linking file candidate parent and offspr
37. ow Additionally there is an example batch file titled batch txt located in the Example Data folder Lines inputting file location information may be specified in one of two ways 1 The entire path of the file may be listed An example line might be C Software PedAgree Demo Parentage output file txt 10 O 2 If the folder housing the batch file is the root directory for the file to be specified then the line can begin with two dots followed by the remainder of the pathway For example if the batch file is located in the Demo file from the example in part 1 then an equivalent input line would be Parentage output file txt Typically a user will not generate batch files by hand because it would take longer than running single output comparisons Instead batch files can be created while running simulations in the program PEDAGOG Coombs et al 2010a and subsequently used by PedAgree Format 1 The first form consists of four lines and is used for the following programs that do not require an ID linking or candidate parent and offspring file s COLONY_V2 SIB COLONY_V2 PAR KINGROUP KINALYZER PEDIGREE GIMLET PAPA PROBMAX and WHICHPARENTS Here is an example Papa True Genotypes Trimmed txt Parentage Assignment PAPA allocation results xls Batch Results Comparison The first line specifies the program Must match spelling on dropdown list The second line specifies the pathway to the true genotype
38. parent designates parents that would be assigned but their probability falls below the relaxed confidence specification All assignments includes the rest of the allocated parents not falling into and of the previous Categories If specifying a CERVUS comparison in a batch file these confidence levels are specified by 0 1 2 and 3 where strict equals 0 relaxed equals 1 most likely equals 2 and all assignments equals 3 Reference Marshall et al 1998 Kalinowski et al 2007 Download http www fieldgenetics com pages home jsp Colony v2 0 Overview Colony is a computer program implementing a maximum likelinood method to assign infer parentage and sibship among individuals using their multi locus genotypes It can be used in estimating full and half sib relationships assigning parentage inferring mating systems polygamous monogamous and reproductive skew in both diploid and haplo diploid species In brief the method model assumes a sample of individuals subdivided into 3 sub samples offspring OFS candidate males CMS and candidate females CFS Individuals in OFS are assigned clustered to K1 paternal and K2 maternal families K1 and K2 unknown individuals in CMS and CFS are assigned paternity and maternity to these K1 and K2 families It is assumed that offspring are either full sibs sharing both parents half sibs sharing only one of the two parents or unrelated sharing no parents while candidates are unre
39. pes of each individual in the sampled population from codominant markers and if available other individual characteristics birth and death dates sex to determine the set of potential mothers potential fathers and potential pairs mothers fathers To determine the set of potential mothers for a given individual the software first checks for each female whether birth and death dates allow this maternity Then it checks for the genetic data compatibility between the individual under consideration and the age compatible females Females or individuals whose sex is unknown that satisfy both compatibility conditions are added to the set of potential mothers The same principle holds for potential fathers For the pairs mothers fathers the software checks the 28 O genetic and age compatibilities for all triplets individual potential mother potential father In each case the program calculates the parentage probability Additional Requirements In order to make the comparison PedAgree requires that the candidate parent and offspring file used to create the PARENTE output file be specified in the Candidate Parent and Offspring File s area When running a PARENTE comparison in PedAgree you will be prompted by the below form for a probability at which to keep the assigned parent Minimum Acceptance Probability Please enter a minimum probability for accepting parent OK pair assignment OK This value m
40. put file from the program selected The Reconstructed Reconstructed Comparison requires output files from the two programs involved Additionally certain programs require a linking file that relates generic labels with actual identifiers or input files to account for which individuals were available for assignment 2 The option buttons allow you to specify if you are going to compare a reconstructed output file against a true known pedigree file compare two reconstructed output files or run a batch file Selection of either Reconstructed True or Reconstructed Reconstructed Comparisons means that the user must lt x x lt specify all of the information mentioned in 1 above Selection for a batch file means that the user must specify the file containing information for a series of output comparisons Batch files can be created by the software PEDAGOG if specified Making them by hand would most likely take longer then running each output individually Selecting the Reconstructed Reconstructed Comparison option makes visible a tab option allowing for the selection of the two relationship reconstruction files to compare If the Reconstructed True Comparison output option is selected then this region of the form specifies the location of the true or known pedigree file At a minimum the file itself must contain three columns offspring dam and sire They must be in that order and they must be separated by tabs The file may c
41. roportion of assignments for instances when the true parent was sampled This is further broken down into categories of correctly assigned incorrectly assigned and incorrectly unassigned 7 The ratio and proportion of assignments for instances when an assignment was made This is further broken down into categories of sampled and correctly assigned sampled and incorrectly assigned and unsampled and incorrectly assigned Below is an example of a parentage assignment summary file Both Parents Absent 34 66 0 5152 One Parent Sampled One Parent Absent 142 208 0 6827 Both Parents Sampled 82 108 0 7593 Summary 258 382 0 6754 Relatedness of misassigned individuals for instances where the true parent was sampled One Parent Sampled One Parent Absent Full Sib 5 41 0 1220 39 Both Parents Sampled Half Sib Non Sib Not Assigned 4 41 0 0976 18 41 0 4390 14 41 0 3415 Full Sib 5 14 0 3571 Half Sib 1 14 0 0714 Non Sib 7 14 0 5000 Not Assigned 1 14 0 0714 Accuracy for instances where at least one parent was assigned but not necessarily present 157 266 0 5902 Accuracy for instances where both parents were assigned but not necessarily present 98 170 0 5765 Assignment proportions for instances where a parent was sampled 157 212 0 7406 Sampled and Incorrectly Assigned 40 212 0 1887 15 212 0 0708 Sampled and Correctly Assigned Sampled and Incorrectly Unassigned
42. s parents with the true parent 4 Not Assigned means that the program did not assign a parent even though the true parent was sampled If sexes are unavailable for the candidate parents then relatedness is compared for all combinations of true and assigned parents and the highest level of relatedness is retained Reconstructed Reconstructed Comparison Individual identifier output 1 assigned parent 1 output 2 assigned parent 1 output 1 assigned parent 2 output 2 assigned parent 2 parent 1 assignment description parent 2 assignment description and score The output 1 assigned parent 1 and 2 identifiers come from the Reconstructed Output 1 file The output 2 assigned parent 1 and 2 identifiers come from the Reconstructed Output 2 file The parent 1 and 2 assignment descriptions describe the comparison between the four assigned parent identifiers There are 2 possible descriptions for a comparison 1 Right means that the output 1 assigned parent equals the output 2 assigned parent 4 Wrong means that the output 1 assigned parent does not equal the output 2 assigned parent Score provides the number of correct comparisons for the individual A score of two means that both assigned parents from output 1 equal their associated assigned parents from output 2 A score of 1 means that one of the assigned parents from output 37 1 equals one of the assigned parents from output 2 while the other assigned parents do not match A score of
43. siblings that must be assigned to a candidate in order to use the candidate as aparent for the entire family Note Each candidate can aes only have a maximum proportion of assigned offspring of 0 5 p 2501 The first output file is a detailed file listing the following information for each individual Individual identifier sibship output file full sib family number sibship output file full sib family size parentage output file full sib family number parentage output file full sib family size and the parentage output file assigned parents Below is an example of a parentage sibship Reconstructed Reconstructed Comparison details file Individual 11852 was assigned to full sib family 1 in the COLONY output file This family was composed of 53 members Based on CERVUS parentage assignment the same individual was assigned to family 2 when parentage was converted to sibship based on shared parents This family was composed of 24 individuals Parents 10080 and 11136 were assigned to this individual in the CERVUS output file ID COLONY FS Family COLONY FS Family Size CERVUS FS Family CERVUS FS Family Size CERVUS Parent 1 CERVUS Parent 2 11852 1 53 2 24 10080 11136 41 11853 1 53 26 1 10080 11137 11857 1 53 2 24 10080 11136 The second file is a summary file and contains the following 1 If the program producing the sibship output was PARENTAGE there will be a line stating the probability level at whi
44. the program simply double click on the PedAgree icon or right click on the PedAgree icon and select Open You will be momentarily presented with the following information screen PedAgree Version 1 04 Last Updated 07 21 2009 Written by Jason A Coombs University of Massachusetts 2008 This screen provides you with the program version number and the date last updated for the executable you are running You can return to this screen at any time by clicking on the About menu option located on the main form Once the information screen departs you are presented with the following main screen H About Output sete A True Pedigree File Program Output File ID Linking File ZE J Ae dsitie das Qa Ba Sa y Huay BKT BPedigreeSimulation E Fri ey Gap BKT 12006 Scoring a Icon template ico V First line contains column headines V First line contains column headinas Results Folder c Hudy BKT Fridley Gap BKT 2 Its Colony a 2 3 Change Results Filename Comparizon 75 Compare 1 The dropdown list allows you to choose which sibship reconstruction or parentage assignment program you wish to evaluate output for Currently there are seventeen choices five for sibship reconstruction and twelve for parentage assignment The Reconstructed True Comparison and Batch File options require a true pedigree file and an out
45. tifiers used by the program to the actual identifiers used in the true pedigree file For each of the seven programs a general overview of what the program does additional requirements needed for PedAgree to make the comparison the reference for the program and a website from which the program can be downloaded are specified Colony v1 2 Overview Colony assigns individuals sampled from a single generation of a population into full sib families nested within half sib families colonies using data on co dominant genetic markers using a maximum likelihood method It can be used in estimating full and half sib relationships inferring mating systems polygamous monogamous and reproductive skew in both diploid and haplo diploid species and reconstructing parental genotypes Additional Requirements In order to make the comparison PedAgree requires an ID linking file Reference Wang 2004 Download http www zsl org science research software colony 1154 AR html Colony v2 0 Overview Colony is a computer program implementing a maximum likelihood method to assign infer parentage and sibship among individuals using their multi locus genotypes It can be used in estimating full and half sib relationships assigning 16 O parentage inferring mating systems polygamous monogamous and reproductive skew in both diploid and haplo diploid species In brief the method model assumes a sample of individuals subdivided into 3
46. to the file one will be added automatically If the Reconstructed True Comparison or Batch File option is selected then output files will have the name of the program producing the output and TRUE Details txt and Summary txt extensions If the Reconstructed Reconstructed Comparison option is selected then output files will have the name of the program producing the first output followed by the name of the program producing the second output followed by Details txt and Summary txt If the comparison is between sibship and parentage output O sources a file with the first and second output program names followed by Pedigree txt is also created v The command buttons labeled 1 2 and 3 will set the results folder text box to the pathway for the selected folder of the true pedigree program output and ID linking candidate parents and offspring respectively 9 The command button labeled Change allows the user to change the results folder pathway Clicking this button opens up the folder selection form seen below P Results Folder Selection Cancel Select Simply select the drive and folder where you want the results file to be stored The command button labeled lt resets the pathway to what was selected when the form opened The command button labeled changes the pathway of the folder up one level The command button labeled New allows for the creat
47. ust be greater than or equal to 0 and less then or equal to 1 If specifying a PARENTE comparison in a batch file the probability value is entered on the seventh line Reference Cercueil et al 2002 Download http Awww leca ujf grenoble fr logiciels htm Pasos Overview 29 O PASOS is a parental allocation program designed to identify collected parents based on individual multilocus genotypes while detecting missing parents when a proportion of them have not been collected It makes use of restricted error tolerance in order to distinguish between a partially incorrect genotype from a false parent s genotype PASOS also introduces the technique of sequence allocation allowing the user to obtain estimates of the proportion of missing parents and of allocation correctness Additional Requirements Be sure to select the allocation results xls file for the program output file Reference Duchesne et al 2005 Download http www2 bio ulaval ca louisbernatchez downloads htm Pedapp Overview PEDAPP calculates a detailed relationship structure typically a pedigree graph or partition and considers it to be the object of inference This makes available tools used in complex model selection theory which have demonstrated effectiveness An important advantage of this approach is that it permits a fully Bayesian approach to the problem providing a principled and accessible way to measure statistical error The approach is de
48. ut to an apparent genotype file that represents a realistic dataset The advantage lies in the fact that PEDAGOG also outputs a true genotype file with parental information for each individual This allows the user to evaluate a sibship reconstruction or parentage assignment program by using an input file created from the apparent genotypes file either specified and made during the PEDAGOG simulation or made post hoc using the input file creation program CREATE Coombs et al 2008 and comparing it to the known pedigree file Additionally PEDAGOG is able to produce a batch file for rapid analysis using PedAgree O For sibship reconstruction comparisons are made between the number and composition of assigned and true full sib families Three scenarios exist for comparison of family number there are fewer assigned families than true families there are more assigned families than true families or the numbers of assigned and true families are equal The first scenario indicates that assignment grouped some true families together while the second scenario indicates that assignment split some families apart The composition of each true family is recovered by listing all the assigned families and their proportion of individuals found in the true family A score is given showing the ratio of individuals assigned to the correct family divided by total individuals For parentage assignment comparisons are made between the assigned and true parents
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