Format conversion software helps a tonne to save biologists in all fields from a huge chunk of manual labor. these few software help us easily convert from one file format to another let it be excel csv, xls format, haploid, diploid format to genepop, arlequin, structure, and many more you name it. These software below are provided strictly for educational purposes only. Some of these software were not available since the websites that hosted them were taken down or the link was not longer available. I do not own any of the software listed below and some of these are hosted on the archive website so it will be useful for future generations. Kindly contact if any author doesn’t want their software to be available here and needs to be taken down.
Create, Convert, Genalex, PGD spider, Formatomatic, Widgetcon. Winboot and Treeview links have been provided below.
Some softwares like widgetcon are online softwares you can access them directly through the link. I have tried to provide the maximum number of tools I have come buy and am pretty sure I have missed out on some. With your suggestions I can improve this list further so do comment below the softwares that you think do deserve to be in this list and share with your friends.
GENETIC DATA FORMAT CONVERSION SOFTWARE
| SOFTWARE | PURPOSE | AUTHOR | LINK |
| CREATE 1.33 | CREATE is software for the creation of new and conversion of existing data input files for 62 genetic data analysis software programs. Programs are grouped into areas of sibship reconstruction, parentage assignment, effective population size, quantitative genetics, general genetic data analysis, and specialized genetic applications. CREATE is able to read in data from text, Microsoft Excel and Microsoft Access sources and allows the user to specify columns containing individual and population identifiers, birth and death data, sex data, relationship information, and spatial location data. CREATE’s only constraints on source data are that one individual is contained in one row, and the genotypic data is contiguous. | 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. | OFFICIAL LINK WORKING LINK |
| CONVERT | convert: A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. convert reads input files in its own ‘standard’ data format, easily produced from an excel file of diploid, codominant marker data, and can convert these to the input formats of the following programs: gda, genepop, arlequin, popgene, microsat, phylip, and structure. convert can also read input files in genepop format. In addition, convert can produce a summary table of allele frequencies in which private alleles and the sample sizes at each locus are indicated. | Jeffrey C. Glaubitz https://doi.org/10.1111/j.1471-8286.2004.00597.x | OFFICIAL LINK WORKING LINK |
| PGD Spider | PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. It facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances). Besides the conventional population genetics formats, PGDSpider integrates population genomics data formats commonly used to store and handle next-generation sequencing (NGS) data. Currently, PGDSpider is not meant to convert very large NGS files as it loads into memory the whole input file, whose size may exceed available RAM. However, since PGDSpider allows one to convert specific subsets of these NGS files into any other format, one could use this feature to calculate parameters or statistics for specific regions, and thus perform sliding window analysis over large genomic regions. | H. E. L. Lischer, L. Excoffier https://doi.org/10.1093/bioinformatics/btr642 | OFFICIAL LINK |
| GENALEX | GenAlEx 6.5 (Peakall and Smouse 2006, 2012) offers a wide range of population genetic analysis options for the full spectrum of genetic markers within the Microsoft Excel environment on both PC and Macintosh computers. When combined with its user-friendly interface, rich graphical outputs for data exploration and publication, tools for data manipulation and export options to many other software packages, we believe that GenAlEx offers an ideal launching pad for population genetic analysis by students, teachers, and researchers alike. | Peakall, R. and Smouse P.E. (2012) GenAlEx 6.5 | OFFICIAL LINK |
| FORMATOMATIC | Population Genetic File Creator and Converter | Manoukis, N.C. 2007. FORMATOMATIC: A program for converting diploid allelic data between common formats for population genetic analysis. Molecular Ecology Notes, In Press. | OFFICIAL LINK |
| WIDGETCON | ONLINE website and program for quick conversion among common population genetic data formats | Aydın M, Kryvoruchko IS, Şakiroğlu M. Widgetcon: A website and program for quick conversion among common population genetic data formats. Mol Ecol Resour. 2019;19:1374–1377. https ://doi.org/10.1111/1755‐0998.13047 | ONLINE LINK OFFICIAL |
| CONVERTF | ANCESTRYMAP EIGENSTRAT PED PACKEDPED PACKEDANCESTRYMAP | Samuela Pollack, Harvard University https://github.com/argriffing/eigensoft/blob/master/CONVERTF/README | LINK |
| GTOOL | GTOOL can be used to: generate subsets of genotype data, to convert genotype data between the PED file format and the file format used by SNPTEST and IMPUTE, merge genotype datasets together, orient genotype data according to a strand file. | Colin Freeman, Jonathan Marchini | LINK |
| Populations 1.2.31 | Converts data files from Genepop to different formats (Genepop, Genetix, Msat, Populations…) | Populations, 1.2.30 Copyright (C) 1999, Olivier Langella, CNRS UPR9034 | LINK |
| WINBOOT | . | https://sites.google.com/site/pbg804/winboot | Working link |
| TREEVIEW | Simple program for displaying phylogenies on Apple Macintosh and Windows PCs. It provides a simple way to view the contents of a NEXUS, PHYLIP, Hennig86, Clustal, or other format tree file. While PAUP and MacClade have excellent tree printing facilities, there may be times you just want to view the trees without having to load the data set they were generated from. | http://taxonomy.zoology.gla.ac.uk/rod/treeview.html | DOWNLOAD LINK |
If you know any more software that is not available in the public domain do comment below me maybe I or the community can help you out. You can reach me at [email protected].
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genetic data format conversion software list
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