| Chapter title |
Marine Genomics
|
|---|---|
| Chapter number | 4 |
| Book title |
Marine Genomics
|
| Published in |
Methods in molecular biology, January 2016
|
| DOI | 10.1007/978-1-4939-3774-5_4 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-3772-1, 978-1-4939-3774-5
|
| Authors |
Cannon, Johanna Taylor, Kocot, Kevin Michael, Johanna Taylor Cannon, Kevin Michael Kocot |
| Editors |
Sarah J. Bourlat |
| Abstract |
This chapter presents a generalized protocol for conducting phylogenetic analyses using large-scale molecular datasets, specifically using transcriptome data from the Illumina sequencing platform. The general molecular lab bench protocol consists of RNA extraction, cDNA synthesis, and sequencing, in this case via Illumina. After sequences have been obtained, bioinformatics methods are used to assemble raw reads, identify coding regions, and categorize sequences from different species into groups of orthologous genes (OGs). The specific OGs to be used for phylogenetic inference are selected using a custom shell script. Finally, the selected orthologous groups are concatenated into a supermatrix. Generalized methods for phylogenomic inference using maximum likelihood and Bayesian inference software are presented. |
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|---|---|---|
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| Unknown | 2 | 67% |
Demographic breakdown
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|---|---|---|
| Members of the public | 2 | 67% |
| Scientists | 1 | 33% |
Mendeley readers
Geographical breakdown
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|---|---|---|
| United Kingdom | 1 | 4% |
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| Unknown | 21 | 91% |
Demographic breakdown
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|---|---|---|
| Researcher | 6 | 26% |
| Student > Ph. D. Student | 5 | 22% |
| Student > Doctoral Student | 3 | 13% |
| Student > Bachelor | 2 | 9% |
| Professor | 2 | 9% |
| Other | 5 | 22% |
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| Medicine and Dentistry | 1 | 4% |
| Other | 1 | 4% |
| Unknown | 1 | 4% |