DNA barcoding: bioinformatics and phylogenetic workflow in R
DNA barcoding is used to (i) assign taxonomic identity to unknown organisms and (ii) obtain taxonomic information about cryptic species. It involves sequencing a fragment of mitochondrial COI gene (=DNA barcodes) from specimens and performing comparisons with a library of DNA barcodes of known taxon...
| Main Authors: | , , |
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| Format: | Book Section |
| Language: | English |
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Elsevier
2025
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| Online Access: | http://psasir.upm.edu.my/id/eprint/116399/ http://psasir.upm.edu.my/id/eprint/116399/1/116399.pdf |
| _version_ | 1848866995364167680 |
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| author | Kanthaswamy, Sree Wilson, John-James Malaivijitnond, Suchinda |
| author_facet | Kanthaswamy, Sree Wilson, John-James Malaivijitnond, Suchinda |
| author_sort | Kanthaswamy, Sree |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | DNA barcoding is used to (i) assign taxonomic identity to unknown organisms and (ii) obtain taxonomic information about cryptic species. It involves sequencing a fragment of mitochondrial COI gene (=DNA barcodes) from specimens and performing comparisons with a library of DNA barcodes of known taxonomy. Here, in an update to the previous edition, we provided step-by-step instructions for using R, an open-source offline platform, to (1) convert sequencing reads into DNA barcodes and (2) analyse the barcodes with phylogenetic trees. We also provided steps of using BOLD, an online COI database, to perform the assignment of taxonomic identity. |
| first_indexed | 2025-11-15T14:29:27Z |
| format | Book Section |
| id | upm-116399 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T14:29:27Z |
| publishDate | 2025 |
| publisher | Elsevier |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-1163992025-04-07T02:11:36Z http://psasir.upm.edu.my/id/eprint/116399/ DNA barcoding: bioinformatics and phylogenetic workflow in R Kanthaswamy, Sree Wilson, John-James Malaivijitnond, Suchinda DNA barcoding is used to (i) assign taxonomic identity to unknown organisms and (ii) obtain taxonomic information about cryptic species. It involves sequencing a fragment of mitochondrial COI gene (=DNA barcodes) from specimens and performing comparisons with a library of DNA barcodes of known taxonomy. Here, in an update to the previous edition, we provided step-by-step instructions for using R, an open-source offline platform, to (1) convert sequencing reads into DNA barcodes and (2) analyse the barcodes with phylogenetic trees. We also provided steps of using BOLD, an online COI database, to perform the assignment of taxonomic identity. Elsevier 2025 Book Section PeerReviewed text en http://psasir.upm.edu.my/id/eprint/116399/1/116399.pdf Kanthaswamy, Sree and Wilson, John-James and Malaivijitnond, Suchinda (2025) DNA barcoding: bioinformatics and phylogenetic workflow in R. In: Encyclopedia of Bioinformatics and Computational Biology (Second Edition). Elsevier, pp. 126-147. ISBN 9780323955034 https://linkinghub.elsevier.com/retrieve/pii/B9780323955027002438 10.1016/B978-0-323-95502-7.00243-8 |
| spellingShingle | Kanthaswamy, Sree Wilson, John-James Malaivijitnond, Suchinda DNA barcoding: bioinformatics and phylogenetic workflow in R |
| title | DNA barcoding: bioinformatics and phylogenetic workflow in R |
| title_full | DNA barcoding: bioinformatics and phylogenetic workflow in R |
| title_fullStr | DNA barcoding: bioinformatics and phylogenetic workflow in R |
| title_full_unstemmed | DNA barcoding: bioinformatics and phylogenetic workflow in R |
| title_short | DNA barcoding: bioinformatics and phylogenetic workflow in R |
| title_sort | dna barcoding: bioinformatics and phylogenetic workflow in r |
| url | http://psasir.upm.edu.my/id/eprint/116399/ http://psasir.upm.edu.my/id/eprint/116399/ http://psasir.upm.edu.my/id/eprint/116399/ http://psasir.upm.edu.my/id/eprint/116399/1/116399.pdf |