PedScope Gold - Advanced Pedigree Analysis
PedScope Gold is a software tool for advanced pedigree analysis, with applications in captive breeding programmes for endangered species conservation and safe breeding practices within closed or small populations such as pedigreed livestock, cats, dogs, etc.
PedScope Gold runs on the Mac, and is obtained through the Mac App Store. A free trial can be downloaded here.
- Computes various pedigree metrics including: Wright's coefficient of inbreeding; ancestral inbreeding coefficients; generation numbers; ancestry metrics including #generations seen, #generations full, #unique ancestors, etc.; relation counts such as #offspring, #sibs, etc.; age-related metrics including generational age, age at death, age at first child, etc. See: Pedigree Metrics.
- Calculates various measures of genetic diversity including: the number of founder equivalents, the number of founder genome equivalents, and the effective number of ancestors, for any user-selected group of individuals that comprise a 'current population'. It can also perform detailed founder analyses for a group and report various details such as the proportion of genes present due to each founder, the genome uniqueness of each founder, and the percentage of each founders genes still present in the current population. It can also compute the mean kinship and kinship value for each individual within the group; metrics useful when making breeding recommendations aimed at retaining long term gene diversity within a population. See: Gene Diversity & Founder Analysis.
- Makes breeding recommendations (i.e. mating recommendations) within a user-selected group of individuals. This is intended to let you compute the best matings in order to meet chosen breeding criteria, and is aimed primarily at those wanting to select matings to maximize future genetic diversity within the ongoing population. Criteria that can be used include: the inbreeding coefficient of the prospective offspring, the change in overall gene diversity ('GD delta') that would result from the mating, the change in overall gene value ('GV delta') that would result from the mating, parental mean kinships, parental kinship values, parental genome uniqueness, and any custom weighted combination of these. See: Breeding Recommendations.
- Reports statistics for groups of individuals, e.g. average inbreeding, or the maximum number of offspring, or the median longevity. These can be produced for any user selected group of individuals. If the source data includes dates/years of birth then stats can be automatically computed for each date period. See: Statistics.
- Generates detailed relations reports, such as ancestors and descendants, either for a single individual, or covering a group of individuals. Ancestor reports can include #occurrences, min/max generation seen, %blood, path length to common ancestors, kinship coefficients to each ancestor, names of founder ancestors, and partial inbreeding coefficients for founder ancestors. See: Relations Reports.
- Lists the litters and the families for any individual. See: Litters & Families.
- Displays individual pedigree charts with highlighting of repeat or common ancestors. See: Pedigree Charts.
- PedScope Gold has comprehensive export and printing facilities. You can print most of the tables created by the program. You can export any data table as PDF, PostScript, text/CSV, XML (for direct import into spreadsheets such as Excel), HTML and Open Document Format (.odt). You can save pedigrees as PDF, PostScript, JPEG, PNG, Scaled Vector Graphics (.svg, for websites), and other bitmap image formats.
- PedScope Gold works with data stored externally in text files (e.g. tab separated, or comma separated (CSV) files). See: Source Data.
- PedScope Gold is a high performance, multithreaded, native application, for both Windows and Mac platforms. It takes full advantage of todays powerful multi-core architectures to carry out extensive background computations whilst retaining a responsive user interface. It can operate with data sets containing millions of records. See: System Requirements.
The full version of PedScope Gold is available exclusively through the Mac App Store. But you can download a free 30 day trial from this site.
A comprehensive user guide is included that can be accessed either online or locally on your computer. If you have any questions just contact us. To be kept informed of updates and changes to PedScope Gold please join our mailing list.
Paid vs. Free Trial
PedScope Gold is available as both a free trial version and a paid version. As you would expect, the paid version has some advantages over the free trial:
- The paid version is not time limited; the free trial is limited to 30 days.
- The paid version works with data files of up to 20,000,000 records. The free trial is limited to 500.
- Export and print facilities within the free trial are disabled (except when used with the bundled examples or simulated pedigrees).
- The paid version includes support and updates.
You can test any of the features of the full version even if you only have the free trial by opening one of several inbuilt pedigree data files (select Examples from the File menu), or by creating a simulated pedigree (select Simulate Pedigree from the File menu).
PedScope Gold computes Wright's coefficient of inbreeding (F) for every animal in a population, either to a fixed depth of ancestry (e.g. 16 generations), or using all ancestry available. Our computation of the inbreeding coefficient is amazingly fast e.g. to compute all inbreeding coefficients to the maximum depth possible for the UK Golden Retriever pedigree - some 500,000+ dogs going back up to 65 generations - took just 7 seconds .
PedScope Gold can also calculate associated pedigree metrics for each individual including: the number of generations ancestors seen, the number of generations that were full (i.e. all ancestors known), the total number of ancestor occurrences seen, the number of unique ancestors, and the pedigree completeness (the % of the pedigree that is known). It can also compute ancestral inbreeding coefficients using the direct method of Ballou  (the ancestral inbreeding coefficient is the cumulative proportion of an individual's genome that has been previously exposed to inbreeding in its ancestors).
The generation number (GN) can be calculated in two different ways. It can either be calculated as one plus the maximum GN of its parents, with founders assigned GN = 0 (as defined by Thompson ), or it can be set as one plus the mean of the GN of the parents (as defined by Brinks et al ). Or you can have both.
Relation counts, including the number of offspring, litters, families, sibs, half sibs, sire sibs, dam sibs, full sibs, #litter sibs can be tabulated. Age-related metrics such as the generational age, age at death, age if living, age at first child, age at last child, age of sire/dam at birth can also be calculated if your input data includes the date/year of birth.
All these individual metrics can be calculated and displayed in the main PedScope Gold window as a table. You can sort the table on any column by clicking the headings.
PedScope Gold also calculate partial inbreeding coefficients and kinship coefficients: see Relations Reports.
Metrics of genetic diversity can be computed for any group of individuals. Typically such a group defines the 'current population', or a subset of current population that is available for breeding. In addition, you choose the depth of ancestry of the group members to be analysed.
PedScope Gold provides various ways to analyse the relationship between any group of individuals and their founders (where a founder is defined as an ancestor that has neither sire nor dam within the ancestry under study).
It will compute the number of founder equivalents, which is the number of equally contributing founders that would be expected to produce the same level of genetic diversity as the group under study, along with the number of founder genome equivalents, which is the number of equally contributing founders with no random loss of alleles in the offspring, that would be expected to produce the same level of genetic diversity as the group under study (i.e., adjusted for genetic drift).
The effective number of ancestors  is a related measure to the above, but which tries to take into account 'bottlenecks' in the pedigree. A separate report will list the most influential ancestors of the group under study that lie behind the number of effective ancestors, together with their marginal contributions.
You can tabulate all the founding ancestors of a group, including columns for the % of the given group's genes due to each founder; the proportion of each founders genes that have been retained within the given group; the genome uniqueness of each founder (i.e. the probability that within the group a given founder's alleles are only inherited by one member of the group). You can then drill down to display a founder contribution matrix that gives the %contribution of each founder to each descendant within the group, or to view the genome uniqueness for each founder with respect to each descendant (i.e., the probability that the given descendant is the only member of the current population that has inherited the respective founder's genes). To compute these metrics PedScope Gold performs a gene drop analysis for the individuals under study and their ancestors .
PedScope Gold can make breeding (mating) recommendations by analysing potential pairings and ordering them according to a single value reflecting the respective merit of the pairing. In this way it can be used as a tool to guide population management decisions. It provides various ways of calculating the merit for each pairing.
Breeders of fancy animals such as dogs and cats are often particularly interested in limiting the inbreeding of the potential offspring. To help with this one of the available measures is simply the coefficient of inbreeding of the offspring. The results can be listed either in a table, ordered by ranking, or as a color-coded matrix of inbreeding coefficients with the sires in columns and the dams in rows. You can immediately see which matings give rise to low or high inbreeding.
In addition to the ranking values it is also possible to list the kinship between each of the prospective parents with a specific known ancestor. For example, breeders of fancy animals are sometimes interested in seeking matings that maximize the influence of particular prized individuals from the past whose influences they are trying to promote in their own breeding lines. I.e. it lets you easily answer the question: against which sire from a group of potential sires should I mate my female against in order to get offspring with the greatest influence from a particular significant ancestor? You simply sort the mate recommendations according to the sire's KC with the significant ancestor and read off the top result.
As with the measures of genetic diversity (above), you use the breeding prediction feature by first defining a group of individuals that represents the available sires and dams, and then you choose the depth of ancestry to be considered in the calculations (including the option of all known ancestry).
The following methods of ranking potential breedings are provided:
- Gene Diversity Delta (GD delta) - this is the change in GD of the population as a result of the addition of a single offspring from the prospective mating. GD is a function of the average mean kinship of the population.
- Gene Value Delta (GV delta) - this is the change in GV of the population as a result of the addition of a single offspring from the prospective mating. GV is a function of the average kinship value of the population.
- Parental MK - this is the average of the parental mean kinships. I.e. the software computes the mean kinship of both sire and dam (with respect to the current population) and then ranks the prospective matings according to the mean of these two values for each pairing. A lower value is better (because, lower values prioritize mating of individuals that share less of their genome in common with the rest of the population).
- Parental MK Delta - this is the difference in the mean kinships of the sire and the dam. It can be detrimental to pair individuals with widely differing mean kinships because this has the effect of combining rare gene lines with over-represented lines.
- Parental Genome Uniqueness - this is the average of the 'genome uniqueness' of the sire and the dam. The 'genome uniqueness' is the total probability, for all founders, that the individual is the only one in the current population containing genes from any one founder. Therefore the higher an individual's 'genome uniqueness', the greater the chance that if that individual is not bred from, then under-represented gene lines will disappear forever from the current population.
- Parental KV - this is the mean of the parental kinship values. The kinship value of an individual is related to the MK, but is weighted according to the age structure of the current population. This can be a better metric upon which to base breeding decisions than the mean kinship, but requires that you also have reproductive values for the different age classes of the current population, and - obviously - you have the age data of the current population. E.g. the current population may include individuals that are past reproductive age. Clearly such animals can never be bred from, so it is better if the genetic diversity contributed by those animals to the current population be discounted when making breeding decisions. Use of KV values enables this.
- Offspring Inbreeding - the inbreeding of the offspring of the prospective mating.
- Composite - this is where a weighted combination of any of the other breeding metrics above, including the offspring inbreeding coefficient, is used. This lets you combine the various measures in whichever way you like, weighted according to the values you wish to prioritize. You can also apply a limit threshold for the offspring inbreeding, so as to remove from the rankings any pairings that would result in excessively highly inbred individuals, irrespective of the other merits of the pairing.
PedScope Gold can compute statistics on groups of individuals.
For each value associated with an individual - such as the coefficient of inbreeding, or the #offspring, or its longevity - PedScope Gold can report the min, max, mean, median, mode, standard deviation, variance and coefficient of variability.
If the source data includes dates/years of birth then the software will automatically compute summary stats for all individuals born in each date period. Periods can be decade, year, quarter, month etc. You can also 'drill down' to see detailed stats for each date period.
In addition it will produce stats for any user-chosen group of individuals. You just tag the individuals of interest then view the summary record details of the tagged set.
PedScope Gold will create detailed reports of relatives such as ancestors, descendants and other relations.
These reports can be produced both for a single individual (e.g. to list all ancestors to a given depth of ancestry for a specific animal), or they can be created for a whole group of individuals at a time, in which case the report is first run separately for all individuals in the group, and the results merged and displayed (e.g., to show all the ancestors of a chosen set of individuals). The grouped report will show the number of times each relative has been seen and associated statistics. E.g. if you run a group ancestors report you can see, for each ancestor, the number of animals in the group of which it is an ancestor, the closest appearance of that ancestor to any of the animals in the group, the maximum % of blood it has to any animal in the group, and so on.
Ancestor reports include: the number of occurrences (of the ancestor in the individual's pedigree), the min/max generation at which the ancestor occurred, overall path lengths if it is a common ancestor, the kinship coefficient between the ancestor and the individual under study, and, if the ancestor is a founder, the partial inbreeding coefficient for that ancestor (the inbreeding due to that founder ancestor). You can order the results using any of the values reported. E.g. to find the founder ancestor with the greatest contribution to inbreeding within a given group of animals you just produce a group ancestors report, then order the table by the partial inbreeding coefficients. Ancestor reports can be limited so they only display the founders, or the common ancestors, of the individual(s) under study.
Descendant reports operate similarly to ancestor reports except they are the 'other way round', and (obviously) do not include details specific to common ancestors and founders.
You can also list all the relatives of an individual (or group) within a given generation span. For this report, PedScope Gold first explores back through the ancestry to find the ancestors to the given depth, and then forward from all ancestors found by the given depth, resulting in a report that includes siblings, uncles/aunts, nephews/nieces, and cousins. You can filter this report to only include particular relations. The genealogical description of the relation (e.g. 'Cousin Twice Removed', 'Half Brother' etc) is given, and you can order the individuals by closeness of relation.
PedScope Gold will list the litters and families of which an individual is a parent. For this purpose we define a litter as being all animals with the same parents and date of birth, and a family as being all animals with the same parents.
PedScope Gold can display simple individual pedigree charts showing the ancestors of an individual up to 6 generations, with optional highlighting of common or repeat ancestors.
PedScope Gold works with data stored externally in text/CSV files. It will work with almost any compatible text file format so long as: (a) the data comprises one line per individual, with columns for different fields; and (b) the columns include, as a minimum, the individual name/ID, sire name/ID and dam name/ID. It can work with data sets comprising many millions of records. Please see System Requirements for more information.
For examples of actual data showing some of the supported input layouts see: Import Data Examples.
The data can optionally include:
- Gender (male/female)
- Date/year of birth
- Date/year of death
- Living 'status' - flag to indicate animals still alive
- Any other columns specific to your data. If these are numeric then PedScope Gold can be configured to produce stats on these values aswell as internally computed values. E.g. if your data has sample measurements such weight, height, etc. then these can be included in stats analyses, correlation charts, etc
NOTE: PedScope Gold does not provide any means to interactively enter data, e.g. to update a pedigree database. At present, the data must be supplied externally in a file.
1. Using Windows 7, 64 bit, AMD Phenom II X6 1035T processor 2.6Gz, 8Gb memory.
2. Ballou, JD. Ancestral Inbreeding Only Minimally Affects Inbreeding Depression in Mammalian Populations, Journal of Heredity 1997, 8:169-178.
3. Thompson, E. Pedigree Analysis in Human Genetics. Johns Hopkins University Press, Baltimore., 1986.
4. Brinks, J., R. Clark, and F. Rice. Estimation of genetic trends in beef cattle, J. Anim.Sci 20: 903, 1962.
5. Lacy, RC. Analysis of founder representation in pedigrees: Founder equivalents and founder genome equivalents. Zoo Biology 8:111-124, 1989.
6. Boichard, D, Maignel L, and Verrier, E. The value of using probabilities of gene origin to measure genetic variability in a population. Genetics Selection Evolution, 1997; 29(1): 5-23.
7. MacCluer, JW, VandeBerg JL, Read B and Ryder OA. Pedigree analysis by computer simulation. Zoo Biology 5, 147/160, 1986.