Forensic Software Resources

MMDIT is a tool for the deconvolution and interpretation of mitochondrial DNA mixtures (whole or partial genomes). The application has an interactive graphical user interface and open source code available on GitHub. This software allows users to deconvolve mixtures into constituent donor haplotypes and estimate random match probabilities on the resultant haplotypes. In cases where deconvolution might not be feasible, the tool allows mixture analysis within a binary framework. Website: https://www.unthsc.edu/mmdit/ Source code: https://github.com/SammedMandape/MMDIT_UI Publication: S.N. Mandape, U. Smart, J.L. King, M. Muenzler, K.B. Kapema, B. Budowle, A.E. Woerner; MMDIT: A tool for the deconvolution and interpretation of mitochondrial DNA mixtures; Forensic Sci. Int. Genet., 55, 2021. https://doi.org/10.1016/j.fsigen.2021.102568 OSIRIS is free, public domain, open source DNA analysis and quality control software that is developed by NCBI at NLM/NIH for STR profile analysis and fragment analysis. Windows and Macintosh versions are available on the OSIRIS homepage, and the source code is available on GitHub. The most recent version of OSIRIS features fragment analysis, which enhances its use for research and home-made marker sets for which there is no allelic ladder. It also features an improved export to facilitate formatting data for export to mixture analysis software. OSIRIS has been validated, and accepted by the FBI, as an expert system for the US National DNA Database (CODIS). OSIRIS is in use in government laboratories for forensic casework, convicted offender testing, and clinical testing for stem cell engraftment. Osiris Homepage https://www.ncbi.nlm.nih.gov/osiris/ GitHub https://github.com/ncbi/osiris Contact email: forensics@ncbi.nlm.nih.gov DNAxs 2.0 is a user-friendly, well-validated software that compares profiles within seconds and proceeds to statistical analysis according to advanced probabilistic models will increase the quality and number of cases that can be handled, and stimulate the use of such advanced statistics. It has been developed by the Netherlands Forensic Institute (NFI) and can be obtained from the NFI upon inquiry: https://www.forensicinstitute.nl/research-and-innovation/international-projects/dnaxs Contact email: DNAxs@NFI.nl LRmix Studio is an open-source, free of charge software dedicated to the interpretation of complex forensic DNA profiles. As a result of the development of DNAxs, no further development is performed on the semi-continuous model LRmix Studio, with the exception of bug fixes. LRmix Studio is no longer available from lrmixstudio.org, but has been migrated to GitHub, from which the software can be downloaded: https://github.com/smartrank/lrmixstudio/releases LRmix Studio is the successor to LRmix. Both programs implement the same model, however LRmix Studio is a more flexible, faster version of LRmix. It can be run on all platforms, and requires Java version 7 or higher. The forensim package for the open source R statistical software is dedicated to forensic DNA mixtures interpretation. It provides tools to simulate mixture cases, and analytical tools to interpret data. The codes have been developed by Hinda Haned (Lyon). http://forensim.r-forge.r-project.org/ Description published by H. Haned: Forensim: An open-source initiative for the evaluation of statistical methods in forensic genetics FSI Genetics 5, 265-268 (2010) DOI Link DNAmixtures (http://dnamixtures.r-forge.r-project.org) is a statistical software for analysing DNA samples from one or multiple donors. It is developed by Therese Graversen and is based on the "fully continuous" statistical model for peak heights described in

• Analysis of forensic DNA mixtures with artefacts. RG Cowell, T Graversen, S Lauritzen, and J Mortera. Journal of the Royal Statistical Society, series C. Volume 64, Issue 1, 1-48, 2015. http://onlinelibrary.wiley.com/doi/10.1111/rssc.12071/full

Key features include

• Likelihood ratios and mixture deconvolution
• Combined analysis of replicates or multiple pieces of DNA evidence
• Visual assessment of the suitability of the model

DNAmixtures offers a new approach to softwares for mixture interpretation; through access to the underlying statistical framework, the user may readily investigate a huge range of "what-if" scenarios. The software is able to run on e.g. a laptop, and it is currently feasible to handle hypotheses with up to 6 unknown contributors. The computations are based on generally applicable exact and efficient methodology described in

• Computational aspects of DNA mixture analysis. T Graversen and S Lauritzen. Statistics and Computing, Volume 25, Issue 3, 527-541. 2015 http://dx.doi.org/10.1007/s11222-014-9451-7

MixtureCalc v1.2 (Freeware version): A free Excel solution to aid the interpretation of mixtures based on both qualitative and quantitative information using data from an exported GeneMapper file (Copyright: Scottish Police Services Authority – submitted by Ben Mallinder). Demonstrated at the Copenhagen Course in Forensic Genetics - June 2010.

• MixtureCalc v1.2 Excel sheet
• License Agreement
• Standard Operation Procedures
• Workshop Examples

Mixture Analysis: A freeware solution to aid the interpretation of mixtures using peak height / or area information using an Excel spreadsheet (Copyright P.D. Gill, Glasgow)

• Excel sheet
• Documentation

likeLTD (likelihoods for low-template DNA profiles) from David Balding described in

• Balding DJ, Buckleton J (2009) Interpreting low template DNA profiles FSI Genetics, 4: 1-10. DOI Link

• Balding DJ (2013) Evaluation of mixed-source, low-template DNA profiles in forensic science. Proc Natl Acad Sci USA 110: 12241–12246. DOI Link

has been updated to version 6.2 in April 2017. The software is written in R. The new version (as well as the previous versions) can be downloaded from https://sites.google.com/site/baldingstatisticalgenetics/software/likeltd-r-forensic-dna-r-code. The software has been expanded with facilities to calculate the weight of the evidence

• when relatives of the alleged contributor are considered,
• with up to 3 unprofiled contributors,
• any number of profiled contributors, each of whom can be analysed as subject to dropout, in which case relative amounts of DNA are estimated, or not subject to dropout, *separate dropout rates for each replicate.

EuroForMix mixture analysis using continuous model EuroForMix is a graphical layer for the functions in the R-package euroformix. The package contains procedures for maximization (frequentistic) and integration (Bayesian) of the likelihood function of a gamma peak height model for single (or replicated) STR/SNP DNA data for a general specifications of hypotheses. Sensitivity analysis of unknown parameters can be carried out using Markov Chain Monte Carlo method. It also contains procedures for deconvolution and database search which may take care of stutters, allele drop-out and allele drop-in; for further details see http://www.euroformix.com

• Ø. Bleka, G. Storvik, P. Gill; EuroForMix: An open source software based on a continuous model to evaluate STR DNA profiles from a mixture of contributors with artefacts; Forensic Sci. Int. Genet., 21:35-44, 2016. DOI Link

T. Tvedebrink's online mixture interpretation tool Torben Tvedebrink's thesis contains a remarkable collection of original publications on population genetics, mixture analysis, and interpretation of results including drop-out events. He has created a DNA Mixture Separator which has been designed to deconvolute 2-person and 3-person mixtures. The algorithms are described in his thesis (link as above) as well as in two publications:

• Evaluating the weight of evidence by using quantitative short tandem repeat data in DNA mixtures. T. Tvedebrink, PS Eriksen, HS Mogensen and N. Morling. Applied Statistics 59(5): 855-874
• Identifying contributors of DNA mixtures by means of quantitative information of STR typing. T. Tvedebrink, PS Eriksen, HS Mogensen and N. Morling. Journal of Computational Biology (in press) (2010)

17.10.2011: The updated version 0.2.1 of Torben's mixture separation software has now been released as a R-package: mixsep. The source files are available at CRAN http://cran.r-project.org/web/packages/mixsep/ including a user manual. Bruce Weir's DNA mixture calculation software DNAMIX3 DNAMIX is a computer program that will calculate likelihood ratios as they pertain to mixed DNA samples encountered in forensic science. Calculations are based on: Curran JM, Triggs CM, Buckleton J. Weir B.S. Interpreting DNA mixtures in structured populations. Journal of Forensic Science 1999;44(5);987-995, and are appropriate for complex mixtures as well as single-contributor stains. http://www.biostat.washington.edu/~bsweir/DNAMIX3/webpage/ FamLink kinship software Andreas Tillmar, Daniel Kling and Thore Egeland have developed a new software, FamLink, which is a user-friendly statistical tool that provides functions for likelihood calculation for family relationships using linked DNA marker data. There is also a paper describing the details in FSI Genetics (2012) FamLink – A user friendly software for linkage calculations in family genetics. The "bracket script" ­– an open source solution for automating a combined composite–consensus method Bram Bekaert and colleagues have published in FSI Genetics an automated method to generate DNA profiles from replicate PCRs by combining advantages of the composite and consensus method by a system of brackets in which an allelic balance threshold is used as a variable to separate DNA-profiles of major from minor donors: Automating a combined composite–consensus method to generate DNA profiles from low and high template mixture samples; FSI Genetics (2012) The authors have written an open source Perl script that they make available together with detailed instructions in the installation and use of this software. All necessary files are zipped together and can be downloaded here: Bracket Script Recommendations 2012 of the ISFG DNA Commission Gill P., Gusmão L., Haned H., Mayr WR., Morling N., Parson W., Prieto L., Prinz M., Schneider H., Schneider PM., Weir BS. (2012), 'DNA commission of the International Society of Forensic Genetics: Recommendations on the evaluation of STR typing results that may include drop-out and/or drop-in using probabilistic methods', Forensic Science International: Genetics 6(6), 679-688 (Gill et al. 2012) Supplementary data available: Excel spreadsheet for LR calculation including dropout and dropin events SmartRank Database Search Software SmartRank is a free open-source (java-based) software dedicated to searching national DNA databases with complex DNA profiles. It is anchored in a Likelihood Ratio framework, and based on the same model behind LRmix Studio. The software and further information can be obtained from http://www.LRmixStudio.org/SmartRank. The SmartRank project was supported by an EU grant (MP2013).