Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format
Abstract Background The STRUCTURE software has gained popularity as a tool for population structure and genetic analysis. Nevertheless, formatting data to meet STRUCTURE's specific requirements can be daunting and susceptible to errors, especially when handling multilocus data. This article hig...
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| Format: | Article |
| Language: | English |
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BMC
2024-02-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-024-05697-7 |
| _version_ | 1797273017274859520 |
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| author | Adam Bessa-Silva |
| author_facet | Adam Bessa-Silva |
| author_sort | Adam Bessa-Silva |
| collection | DOAJ |
| description | Abstract Background The STRUCTURE software has gained popularity as a tool for population structure and genetic analysis. Nevertheless, formatting data to meet STRUCTURE's specific requirements can be daunting and susceptible to errors, especially when handling multilocus data. This article highlights the creation of a graphical user interface (GUI) application tailored to streamline the process of converting multiple sequence alignments into a single, cohesive file that is compatible with the STRUCTURE software. Results The application has been developed utilizing Tkinter for the GUI and Biopython for handling FASTA files. This program processes the files, pinpoints variable sites, and converts the sequences into a binary format. Subsequently, the sequences are concatenated and presented within the graphical interface's text area, enabling users to review and confirm the results. Furthermore, the program stores the concatenated results in a file, delivering a ready-to-use input for the STRUCTURE software. Conclusion This application offers an efficient and dependable solution for transforming multiple aligned FASTA files into a concatenated binary format file, which is compatible with the STRUCTURE software. With its user-friendly graphical interface and error-reduction approach, this tool proves invaluable for researchers engaged in population structure and genetic analysis. |
| first_indexed | 2024-03-07T14:37:32Z |
| format | Article |
| id | doaj.art-1894975a1e8d4adcb382552427dbc3c9 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-03-07T14:37:32Z |
| publishDate | 2024-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-1894975a1e8d4adcb382552427dbc3c92024-03-05T20:31:41ZengBMCBMC Bioinformatics1471-21052024-02-012511810.1186/s12859-024-05697-7Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE formatAdam Bessa-Silva0Laboratório de Evolução, Universidade Federal do ParáAbstract Background The STRUCTURE software has gained popularity as a tool for population structure and genetic analysis. Nevertheless, formatting data to meet STRUCTURE's specific requirements can be daunting and susceptible to errors, especially when handling multilocus data. This article highlights the creation of a graphical user interface (GUI) application tailored to streamline the process of converting multiple sequence alignments into a single, cohesive file that is compatible with the STRUCTURE software. Results The application has been developed utilizing Tkinter for the GUI and Biopython for handling FASTA files. This program processes the files, pinpoints variable sites, and converts the sequences into a binary format. Subsequently, the sequences are concatenated and presented within the graphical interface's text area, enabling users to review and confirm the results. Furthermore, the program stores the concatenated results in a file, delivering a ready-to-use input for the STRUCTURE software. Conclusion This application offers an efficient and dependable solution for transforming multiple aligned FASTA files into a concatenated binary format file, which is compatible with the STRUCTURE software. With its user-friendly graphical interface and error-reduction approach, this tool proves invaluable for researchers engaged in population structure and genetic analysis.https://doi.org/10.1186/s12859-024-05697-7STRUCTURE formatMultiple FASTA filesTkinterBiopythonAligned sequencesPopulation genetics |
| spellingShingle | Adam Bessa-Silva Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format BMC Bioinformatics STRUCTURE format Multiple FASTA files Tkinter Biopython Aligned sequences Population genetics |
| title | Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format |
| title_full | Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format |
| title_fullStr | Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format |
| title_full_unstemmed | Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format |
| title_short | Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format |
| title_sort | fasta2structure a user friendly tool for converting multiple aligned fasta files to structure format |
| topic | STRUCTURE format Multiple FASTA files Tkinter Biopython Aligned sequences Population genetics |
| url | https://doi.org/10.1186/s12859-024-05697-7 |
| work_keys_str_mv | AT adambessasilva fasta2structureauserfriendlytoolforconvertingmultiplealignedfastafilestostructureformat |