Systematics Section / ASPT
Caujape-Castells, Juli , Baccarani-Rosas, Mario .
Surfing matrices of any size, error-free and in no time: Transformer-3, a software for boosting molecular population genetic data analyses.
AFTER completing molecular analyses and gel interpretations, population geneticists are confronted with the onerous task of formatting huge matrices and run them into different calculation programs whose input files are complex, heterogeneous and (in most cases) incompatible. This process often becomes too long, it unavoidably begets mistakes, and it spends a considerable amount of research effort in the wrong direction. This contribution introduces the present capabilities and the foreseeable future of Transformer-3, a free software that allows the researcher to swiftly analyse raw molecular population genetic data for co-dominant (allozymes, microsatellites) and dominant (AFLP, RAPD, RFLPs, PCR-RFLPs) markers for a practically unlimited number of individuals and loci using 13 programs of widespread use in population genetics. The performance of Transformer-3 was tested with data for 17 Canarian plant endemics corresponding to 1.189 individuals grouped in 121 populations (see ID:142 and ID:144 for two examples). The 17 data matrices included 1.450 dominant loci and 14 co-dominant ones, and their analyses entailed a total of 50 different population groupings, encompassing the generation of files for four programs (Arlequin, Popgene, NTSYS, and GenePop for dominant data, and BIOSYS, Popgene, NTSYS and Genestat for co-dominant data) plus a PCA for each dominant dataset. Using Transformer-3, these analyses were completed in 10 hours and 20 minutes. Based on previous experience without Transformer-3, we estimate that they would have taken four months of work (8 hours a day, 5 days per dataset = 17 weeks) of a specialised scientist (resting weekends). Thus, we reckon that Transformer-3 can boost data analyses at least 100-fold, thereby allowing the researcher to devote his/her time to what really matters: the critical discussion of results and hypotheses. Transformer-3 was developed in the absence of funding via a collaboration between the Jardín Botánico Canario “Viera y Clavijo” and EXEGEN software.
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free downloads of Transformer-3 (1)
free downloads of Transformer-3 (2)
1 - Jardín Botánico Canario \"Viera y Clavijo\", Molecular Biodiversity Labs and DNA Bank, Ap. de correos 14 de Tafira Alta., Las Palmas de Gran Canaria, 35017, Spain
population genetics data
dominant and codominant data
unlimited matrix size.
Presentation Type: Poster:Posters for Sections
Location: Auditorium/Bell Memorial Union
Date: Tuesday, August 1st, 2006
Time: 12:30 PM