GenoDup Pipeline: a tool to detect genome duplication using the dS-based method
Understanding whole genome duplication (WGD), or polyploidy, is fundamental to investigating the origin and diversification of organisms in evolutionary biology. The wealth of genomic data generated by next generation sequencing (NGS) has resulted in an urgent need for handy and accurate tools to de...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2019-01-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/6303.pdf |
| _version_ | 1797417639183646720 |
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| author | Yafei Mao |
| author_facet | Yafei Mao |
| author_sort | Yafei Mao |
| collection | DOAJ |
| description | Understanding whole genome duplication (WGD), or polyploidy, is fundamental to investigating the origin and diversification of organisms in evolutionary biology. The wealth of genomic data generated by next generation sequencing (NGS) has resulted in an urgent need for handy and accurate tools to detect WGD. Here, I present a useful and user-friendly pipeline called GenoDup for inferring WGD using the dS-based method. I have successfully applied GenoDup to identify WGD in empirical data from both plants and animals. The GenoDup Pipeline provides a reliable and useful tool to infer WGD from NGS data. |
| first_indexed | 2024-03-09T06:22:41Z |
| format | Article |
| id | doaj.art-40e4c46bd7d94edf990f7a1ef454626d |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:22:41Z |
| publishDate | 2019-01-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-40e4c46bd7d94edf990f7a1ef454626d2023-12-03T11:33:58ZengPeerJ Inc.PeerJ2167-83592019-01-017e630310.7717/peerj.6303GenoDup Pipeline: a tool to detect genome duplication using the dS-based methodYafei Mao0Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, JapanUnderstanding whole genome duplication (WGD), or polyploidy, is fundamental to investigating the origin and diversification of organisms in evolutionary biology. The wealth of genomic data generated by next generation sequencing (NGS) has resulted in an urgent need for handy and accurate tools to detect WGD. Here, I present a useful and user-friendly pipeline called GenoDup for inferring WGD using the dS-based method. I have successfully applied GenoDup to identify WGD in empirical data from both plants and animals. The GenoDup Pipeline provides a reliable and useful tool to infer WGD from NGS data.https://peerj.com/articles/6303.pdfPolyploidyWhole-genome duplication (WGD)dS-basedNext generation sequencing (NGS)SoftwareAge distribution |
| spellingShingle | Yafei Mao GenoDup Pipeline: a tool to detect genome duplication using the dS-based method PeerJ Polyploidy Whole-genome duplication (WGD) dS-based Next generation sequencing (NGS) Software Age distribution |
| title | GenoDup Pipeline: a tool to detect genome duplication using the dS-based method |
| title_full | GenoDup Pipeline: a tool to detect genome duplication using the dS-based method |
| title_fullStr | GenoDup Pipeline: a tool to detect genome duplication using the dS-based method |
| title_full_unstemmed | GenoDup Pipeline: a tool to detect genome duplication using the dS-based method |
| title_short | GenoDup Pipeline: a tool to detect genome duplication using the dS-based method |
| title_sort | genodup pipeline a tool to detect genome duplication using the ds based method |
| topic | Polyploidy Whole-genome duplication (WGD) dS-based Next generation sequencing (NGS) Software Age distribution |
| url | https://peerj.com/articles/6303.pdf |
| work_keys_str_mv | AT yafeimao genoduppipelineatooltodetectgenomeduplicationusingthedsbasedmethod |