Next-generation phylogenomics
<p>Abstract</p> <p>Thanks to advances in next-generation technologies, genome sequences are now being generated at breadth (<it>e.g.</it> across environments) and depth (thousands of closely related strains, individuals or samples) unimaginable only a few years ago. <...
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| Format: | Article |
| Language: | English |
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BMC
2013-01-01
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| Series: | Biology Direct |
| Subjects: | |
| Online Access: | http://www.biology-direct.com/content/8/1/3 |
| _version_ | 1818149862082871296 |
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| author | Chan Cheong Xin Ragan Mark A |
| author_facet | Chan Cheong Xin Ragan Mark A |
| author_sort | Chan Cheong Xin |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Thanks to advances in next-generation technologies, genome sequences are now being generated at breadth (<it>e.g.</it> across environments) and depth (thousands of closely related strains, individuals or samples) unimaginable only a few years ago. <it>Phylogenomics</it> – the study of evolutionary relationships based on comparative analysis of genome-scale data – has so far been developed as industrial-scale molecular phylogenetics, proceeding in the two classical steps: multiple alignment of homologous sequences, followed by inference of a tree (or multiple trees). However, the algorithms typically employed for these steps scale poorly with number of sequences, such that for an increasing number of problems, high-quality phylogenomic analysis is (or soon will be) computationally infeasible. Moreover, next-generation data are often incomplete and error-prone, and analysis may be further complicated by genome rearrangement, gene fusion and deletion, lateral genetic transfer, and transcript variation. Here we argue that next-generation data require next-generation phylogenomics, including so-called <it>alignment-free</it> approaches.</p> <p>Reviewers</p> <p>Reviewed by Mr Alexander Panchin (nominated by Dr Mikhail Gelfand), Dr Eugene Koonin and Prof Peter Gogarten. For the full reviews, please go to the Reviewers’ comments section.</p> |
| first_indexed | 2024-12-11T13:13:46Z |
| format | Article |
| id | doaj.art-1f3bdadb5ba641598168cff4bbca5dee |
| institution | Directory Open Access Journal |
| issn | 1745-6150 |
| language | English |
| last_indexed | 2024-12-11T13:13:46Z |
| publishDate | 2013-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Biology Direct |
| spelling | doaj.art-1f3bdadb5ba641598168cff4bbca5dee2022-12-22T01:06:06ZengBMCBiology Direct1745-61502013-01-0181310.1186/1745-6150-8-3Next-generation phylogenomicsChan Cheong XinRagan Mark A<p>Abstract</p> <p>Thanks to advances in next-generation technologies, genome sequences are now being generated at breadth (<it>e.g.</it> across environments) and depth (thousands of closely related strains, individuals or samples) unimaginable only a few years ago. <it>Phylogenomics</it> – the study of evolutionary relationships based on comparative analysis of genome-scale data – has so far been developed as industrial-scale molecular phylogenetics, proceeding in the two classical steps: multiple alignment of homologous sequences, followed by inference of a tree (or multiple trees). However, the algorithms typically employed for these steps scale poorly with number of sequences, such that for an increasing number of problems, high-quality phylogenomic analysis is (or soon will be) computationally infeasible. Moreover, next-generation data are often incomplete and error-prone, and analysis may be further complicated by genome rearrangement, gene fusion and deletion, lateral genetic transfer, and transcript variation. Here we argue that next-generation data require next-generation phylogenomics, including so-called <it>alignment-free</it> approaches.</p> <p>Reviewers</p> <p>Reviewed by Mr Alexander Panchin (nominated by Dr Mikhail Gelfand), Dr Eugene Koonin and Prof Peter Gogarten. For the full reviews, please go to the Reviewers’ comments section.</p>http://www.biology-direct.com/content/8/1/3PhylogenomicsMultiple sequence alignmentAlignment-free methods<it>k</it>-mersHomology signal |
| spellingShingle | Chan Cheong Xin Ragan Mark A Next-generation phylogenomics Biology Direct Phylogenomics Multiple sequence alignment Alignment-free methods <it>k</it>-mers Homology signal |
| title | Next-generation phylogenomics |
| title_full | Next-generation phylogenomics |
| title_fullStr | Next-generation phylogenomics |
| title_full_unstemmed | Next-generation phylogenomics |
| title_short | Next-generation phylogenomics |
| title_sort | next generation phylogenomics |
| topic | Phylogenomics Multiple sequence alignment Alignment-free methods <it>k</it>-mers Homology signal |
| url | http://www.biology-direct.com/content/8/1/3 |
| work_keys_str_mv | AT chancheongxin nextgenerationphylogenomics AT raganmarka nextgenerationphylogenomics |