Roadmap to the study of gene and protein phylogeny and evolution—A practical guide
Jacques, Florian LU ; Bolivar, Paulina LU ; Pietras, Kristian LU
and Hammarlund, Emma U.
LU
(2023)
In PLoS ONE
18(2).
- Abstract
Developments in sequencing technologies and the sequencing of an ever-increasing number of genomes have revolutionised studies of biodiversity and organismal evolution. This accumulation of data has been paralleled by the creation of numerous public biological databases through which the scientific community can mine the sequences and annotations of genomes, transcriptomes, and proteomes of multiple species. However, to find the appropriate databases and bioinformatic tools for respective inquiries and aims can be challenging. Here, we present a compilation of DNA and protein databases, as well as bioinformatic tools for phylogenetic reconstruction and a wide range of studies on molecular evolution. We provide a protocol for information... (More)
Developments in sequencing technologies and the sequencing of an ever-increasing number of genomes have revolutionised studies of biodiversity and organismal evolution. This accumulation of data has been paralleled by the creation of numerous public biological databases through which the scientific community can mine the sequences and annotations of genomes, transcriptomes, and proteomes of multiple species. However, to find the appropriate databases and bioinformatic tools for respective inquiries and aims can be challenging. Here, we present a compilation of DNA and protein databases, as well as bioinformatic tools for phylogenetic reconstruction and a wide range of studies on molecular evolution. We provide a protocol for information extraction from biological databases and simple phylogenetic reconstruction using probabilistic and distance methods, facilitating the study of biodiversity and evolution at the molecular level for the broad scientific community.
(Less)
- author
- Jacques, Florian
LU
; Bolivar, Paulina
LU
; Pietras, Kristian
LU
and Hammarlund, Emma U.
LU
- organization
- publishing date
- 2023
- type
- Contribution to journal
- publication status
- published
- subject
- in
- PLoS ONE
- volume
- 18
- issue
- 2
- article number
- e0279597
- publisher
- Public Library of Science (PLoS)
- external identifiers
-
- pmid:36827278
- scopus:85148865334
- ISSN
- 1932-6203
- DOI
- 10.1371/journal.pone.0279597
- language
- English
- LU publication?
- yes
- id
- 6e0bcd7d-b5d6-4bf5-b888-6846d057f17b
- date added to LUP
- 2023-03-21 10:49:15
- date last changed
- 2024-06-14 00:40:19
@article{6e0bcd7d-b5d6-4bf5-b888-6846d057f17b,
abstract = {{<p>Developments in sequencing technologies and the sequencing of an ever-increasing number of genomes have revolutionised studies of biodiversity and organismal evolution. This accumulation of data has been paralleled by the creation of numerous public biological databases through which the scientific community can mine the sequences and annotations of genomes, transcriptomes, and proteomes of multiple species. However, to find the appropriate databases and bioinformatic tools for respective inquiries and aims can be challenging. Here, we present a compilation of DNA and protein databases, as well as bioinformatic tools for phylogenetic reconstruction and a wide range of studies on molecular evolution. We provide a protocol for information extraction from biological databases and simple phylogenetic reconstruction using probabilistic and distance methods, facilitating the study of biodiversity and evolution at the molecular level for the broad scientific community.</p>}},
author = {{Jacques, Florian and Bolivar, Paulina and Pietras, Kristian and Hammarlund, Emma U.}},
issn = {{1932-6203}},
language = {{eng}},
number = {{2}},
publisher = {{Public Library of Science (PLoS)}},
series = {{PLoS ONE}},
title = {{Roadmap to the study of gene and protein phylogeny and evolution—A practical guide}},
url = {{http://dx.doi.org/10.1371/journal.pone.0279597}},
doi = {{10.1371/journal.pone.0279597}},
volume = {{18}},
year = {{2023}},
}