Download
The Familias software, downloaded below, runs under Windows (Tested on Windows XP, 7 and 10). Works on other systems with emulated Windows environment. Familias may be run under Mac OS using an emulated Windows environment (for instance through Wine), our colleague Elias Hernadis has posted an excellent walkthrough.
Download the latest version 3.3.1 (Release 2022-09-30)
Download Familias pedigree plotting tool (Released 2017-03-11)
Old versions
Download the latest version 3.3 (Release 2021-12-09)
Download the latest version 3.2.9 (Pre-release 2020-12)
Download the latest version 3.2.8 (Released 2019-08-23)
Download version 3.2.7 (Release 2019-06-20)
Download version 3.2.6 (Release 2019-04-30)
Download version 3.2.5 (Release 2019-01-29)
Download version 3.2.4 (Release 2018-11-29 - an early version was released 2018-11-23 with a minor bug)
Download version 3.2.3 (Early release 2018-08-30)
Download version 3.2.2 (Release 2017-12-21)
Download version 3.2.1 (Release 2017-05-08)
Download version 3.2 (Released 2017-03-07)
Download version: 3.1.9.8 (Released 2016-10-xx)
Download version: 3.1.9.6 (Released 2016-09-19)
Download version: 3.1.9.5 (Released 2016-07-28)
Download version: 3.1.9.4 (Released 2016-04-27)
Download version: 3.1.9.3 (Released 2016-03-01)
Download version: 3.1.9.2 (Released 2015-11-24)
Download version: 3.1.9.1 (Released 2015-11-20)
Download version: 3.1.9 (Released 2015-10-26)
Create pedigree plots (FamiliasPedigreeCreator)
A new tool has been developed that will create pedigree plots for all pedigrees in a specified folder. Below is a link to the software as well as getting started instructions. The software also require the software R to be installed.
FamiliasPedigreeCreator (v 1.1) - Can handle DVI and "normal" Familias projects
FamiliasPedigreeCreator (v 1.0) - Can only handle "normal" Familias projects
Databases
Users will be able to download databases prepared in the Familias (> version 3.0) in this section. Currents users are encouraged to share their Familias frequency database if possible. The allele frequencies are freely available through several online sites as well as usually available from supplementary files in papers on population data. Familias can easily import frequency data on the standard allele/marker matrix format.
From NIST 1036, we have compiled a set of databases from the 2017 revision. N represents the number of individuals.
From pop STR (see for instance Phillips et al.) we have compiled databases for 4 mayor population groups containing data for up to 70 STR markers. Details below and in previously mentioned reference.
Validation
The following files can be used to validate new versions of Familas. Results appear in this file. See also the paper
Familias 3 - Extensions and new functionality
Installation instructions
The latest version of Familias will install for most Windows PC:s. For Apple users, and other OS users, a Windows environment can be simulated. In contrast to previous version (<2.0), the new Familias does not rely on .dll files and can be used as a stand-alone software, i.e. the software can be run from a USB drive. The installation should be straightforward. Should any difficulties be encountered the user are encouraged to contact Daniel Kling. (For installation instructions on the old versions, please see http://familias.name)
English and Spanish instruction videos available here.
There has been several incidents of anti-virus software (particularly Symantec products) reporting Familias installation as a threat. This is a false alarm and has been forwarded to Symantec. Users are advised to ignore the message and run the installation anyway. If the error persists or if the installation fails, it may be that administrator rights are needed. The false alarm is caused by the fact that the new Familias is not a widely known software (even though it has quite some users), and as a new line in the defense against new threats the anti-virus software has implemented algorithms to search for "new, unknown" software/code.
Updates in Familias 3.3 and 3.3.1
- Fixed several bugs
- Increased the maximum size of familial searching databases to 1 million profiles
- Improved several things in the DVI module. Missing person genders are now properly saved
- The Global search function in the DVI module is still not fully implemented and should only be used for research purposes.
Updates in Familias 3.2.9
- Fixed several bugs
- Improved speed in some dialogs when handling large data sets.
- Familias can now better interpret relationship in the DVI module (Import multiple reference families)
- Improved support for importing allele frequency databases. Import now gives a message if allele frequencies do not sum to 1.
- Improvements to memory handling in the familias searching module. It should now be possible to import databases of up to 10,000,000 profiles.
- Generate pedigree window now has an option to remove redundant pedigree, essentially discarding pedigrees that is redundant if mutations are not considered.
- The DVI module now allows the definition of multiple missing persons within the same pedigree. The function wil in the next release (3.3) allow a complete search for all possible combination of missing persons and PM data, what we refer to as a Global search.
- Import of xml-files in the DVI module now recognizes a SPECIMENDVI tag that may contain AM or PM specific name tags.
- Global search function, accessed through DVI module -> Reference families. This function will not be released in version 3.2.9 but is implemented for early alpha testing of some functionality. Will be fully released in version 3.3
- Adding entities in the DVI module is now possible. An entity is defined as a set of individuals (known) representing an unidentified individual. Adding entities is possible in the Unidentified person dialog. Essentially this allows one to define a family with individuals, related to an individual that may be missing. As an example, this may be relevant in missing person cases where a family suspects that their father is a missing person.
- Some changes made to the dialog where reference families are edited (DVI module).
- Import pedigrees. Yes, correct (!), you can now import pedigrees on the LINKAGE format. Create them graphically at https://magnusdv.shinyapps.io/quickped/ and export without Headers and with Family ID. Alternatively create the .ped file manually according to instructions at http://csg.sph.umich.edu/abecasis/merlin/tour/input_files.html.
Updates in Familias 3.2.8
- Fixed some minor bugs
- Included option in the DVI module to change the posterior model. More information will follow shortly in the updated tutorial.
Updates in Familias 3.2.7
- Fixed a bug that caused the Create database function to crash when importing data in Genemapper format.
- Fixed a bug that caused Familias not to save data in the DVI module
- Fixed a bug that caused some errors when importing a frequency database from text file and then importing case DNA data.
- Improved the allele lumping feature - activated through the Advanced dialog (will be presented at the ISFG2019 conference in Prague). It will work both for pedigrees in the normal mode as well as in the DVI module of Familias.
- Changed the results display in the DVI module where all results will be displayed if LR=0 is chosen as threshold.
Updates in Familias 3.2.6
- Fixed a bug when importing Genemapper data. The bug would sometimes wrongly assign incorrect alleles whenever duplicates samples were imported.
Updates in Familias 3.2.5
- Fixed several bugs (some listed below)
- Generate pedigree function with extra persons yielded bad results Checking relations in pedigrees (DVI module) updated. Bug reported bad relations. Prior computation (DVI module) updated. Results could be slightly in previous versions due to priors being computed using integers instead of floats. Sorting and listing of results in the DVI module updated. Version 3.2.4 contained a bug that listed results backwards.
- Generate pedigree function with extra persons yielded bad results
- Checking relations in pedigrees (DVI module) updated. Bug reported bad relations.
- Prior computation (DVI module) updated. Results could be slightly in previous versions due to priors being computed using integers instead of floats.
- Sorting and listing of results in the DVI module updated. Version 3.2.4 contained a bug that listed results backwards.
Updates in Familias 3.2.4
- New allele dialog updated - It is now possible to remember choice such that all new alleles are added with the current setting.
- Conditional simulations available - Available through the pedigrees window
- Blind search - Minor updates to the interface. Minor allele frequency implemented in the comparisons
- Updates in the Familial searching interface.
- Minor bugs corrected Possibility to find the maximum likelihood estimate of relationship Minor allele frequency implemented in the search
- Minor bugs corrected
- Possibility to find the maximum likelihood estimate of relationship
- Minor allele frequency implemented in the search
Updates in Familias 3.2.2
- Several dialogs will now display red colored text when a mismatch is detected.
- Blind search dialog for parent/child and direct matches. Merge profiles/samples dialog DVI search dialog Evaluate reference family View reference family with DNA data and pedigree
- Blind search dialog for parent/child and direct matches.
- Merge profiles/samples dialog
- DVI search dialog
- Evaluate reference family
- View reference family with DNA data and pedigree
- When importing and displaying reference families within the DVI module, Familias will perform some elementery controls,
- Is there at least two pedigrees defined for a specific family? If no, the family is marked with red Is there at least one genotyped reference family member (data) with a relation in a pedigree? If no, the family is marker with red Is there a typed reference family member with no relation in a pedigree the family is marked orange.
- Is there at least two pedigrees defined for a specific family? If no, the family is marked with red
- Is there at least one genotyped reference family member (data) with a relation in a pedigree? If no, the family is marker with red
- Is there a typed reference family member with no relation in a pedigree the family is marked orange.
- Minor updates to some windows
- DVI search dialog displays mismatches Blind search displays mismatches
- DVI search dialog displays mismatches
- Blind search displays mismatches
- Included the ability to change the priors in the Pedigrees dialog, warning message displayed if not sum to one.
- New import feature for databases: Use the matrix/table format often described in publications, i.e. markers are listed in the first row, with Alleles in the first column. Identifier "Alleles" need to be present in the first cell/element of the table in order for Familias to detect the format.
- Increased the size of some windows
- The import of reference families in the DVI module is now more thoroughly checked. Familias will give warnings to families where some error is detected.
- Minor changes, removed some warnings.
- The blind search interface has been updated. Familias can now cluster matches, i.e. locate and group samples that are connected. Conditional coloring is also available.
- The blind search interface now displays some IBS metrics.
- Secondary sort key now works properly in the blind search dialog
- Added support for carrige return (Enter key) in several dialogs. Default action is to close the window (without saving changes). Now some dialogs will Add new person/allele/relation when the Enter key is pressed instead.
- Plotting a pedigree will now also generate a png file (in a Pedigree plots subfolder) that may be viewed in Familias.
Updates in Familias 3.2.1
- The XML saving function is now improved allowing to save DVI project and files with Merged profiles.
- Corrected some minor bugs in the DVI module
- Improved the merging function. Now when merging profiles profiles will be displayed and the ending profile may be a combination of the two merged ones.
- Some minor improvements to the plotting function.
- Further corrections of some incorrectly recognized relationships in the "Import reference family" function of the DVI module.
Updates in Familias 3.2
- Corrected some bugs detected when switching databases in Familias. Switching could cause a crash or wrong genotypes of individuals.
- Further improvements when importing large xml databases in the familial searching module.
- Greatly improved speed and memory handling in the blind search interface.
- Update to the Direct-matching function in the blind search module. Dropout/Dropin/typing errors are now also considered in the denominator.
- Information about merged profiles are now stored and can be viewed via Tools->Merged profiles. Reports may be generated as well as undoing a merge if necessary.
- Corrected a bug that made the force minor allele frequency function not to work. For users not familiar with this feature, it allows you to force the frequencies to sum to more than 1 by using a specific MAF for each marker.
- Exciting new feature in the DVI module: Evalute each families potential to identify a missing person (Paper in preparation). This feature allows you to perform simulation on all reference families in a DVI project to obtain all kinds of different information. We must admit, a really nice new feature.
- Some minor bugs corrected in the DVI module.
- Users may now run a Mendelian inheritance check on any family in the DVI module.
- Save a project as xml (Beta). This works both as a report when LR computations have been done or use the Save as function to save the whole project. Does not work on DVI or Familial searching projects yet.
- Greatly enhanced plotting functions, please see complete section in Manual.
- Lumping of alleles is now allowed within the Advanced dialog. (File -> Advanced). This is currently in early Alpha testing. Briefly it allows the user to specify a threshold. This threshold applies to the probability to mutate (i.e. to observe) an allele not observed in the case data. This way even the mutation matrix for the extended stepwise model can be condensed without any bigger changes to the likelihood. We refer to future version of Familias where this feature will be explained more in detail.
Updates in Familias 3.1.9.6
- Corrected some minor bugs in the DVI module
- Improved the plotting function for pedigrees
- Plot genotypes of persons usingt the R-export function
- Search only selected persons and families in the DVI module
- Include IBS parameters in the familial searching module.
- Corrected some bugs in the import features (both reference families and xml files)
Updates in Familias 3.1.9.5
- Fixed some bugs in the Familias searching module causing a crash when importing xml files
- Plotting pedigrees function has been further improved
- Sorting functions in the DVI module to sort reference families and unidentified persons
- Bug that appared when building DVI reports has now been fixed
- NA (Not applicable) will now appear as the LR when scaling against a pedigree with zero likelihood
- Markers with the same name can no longer be defined
- Some corrections to the proportional mutation model have been made
- Fixed some other minor bugs
Updates in Familias 3.1.9.4
- Quick fix of some minor bugs that appeared in the previous version
- Plotting pedigrees function has been improved.
- Fixed some bugs in the plotting function.
- Advanced settings are now saved to the project file.
- Added extra column in the DVI results window. Now the number of mismatches (i.e. likelihood=0) is displayed.
- Some minor cosmetic changes
Updates in Familias 3.1.9.3
- Several mayor updates to the Familias searching interface. A paper including a validation of this interface has been submitted.
- New import format in the DVI module now available for reference family data: Familias projects. Import Familias projects containing complete data with pedigrees.
- Plot pedigrees feature now available. Requires the freeware R to be installed together with the Familias package. Feature available when editing pedigrees.
- Removed a bug that could cause bad data import when detecting new/unseen alleles.
- New export functions in the DVI module
- Several minor bugs smashed.