PhyloFisher: A phylogenomic package for resolving eukaryotic relationships.
Phylogenomic analyses of hundreds of protein-coding genes aimed at resolving phylogenetic relationships is now a common practice. However, no software currently exists that includes tools for dataset construction and subsequent analysis with diverse validation strategies to assess robustness. Furthe...
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2021
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oai:doaj.org-article:5458e9e481234510ae6f912b55e8b0bb2021-12-02T19:54:40ZPhyloFisher: A phylogenomic package for resolving eukaryotic relationships.1544-91731545-788510.1371/journal.pbio.3001365https://doaj.org/article/5458e9e481234510ae6f912b55e8b0bb2021-08-01T00:00:00Zhttps://doi.org/10.1371/journal.pbio.3001365https://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885Phylogenomic analyses of hundreds of protein-coding genes aimed at resolving phylogenetic relationships is now a common practice. However, no software currently exists that includes tools for dataset construction and subsequent analysis with diverse validation strategies to assess robustness. Furthermore, there are no publicly available high-quality curated databases designed to assess deep (>100 million years) relationships in the tree of eukaryotes. To address these issues, we developed an easy-to-use software package, PhyloFisher (https://github.com/TheBrownLab/PhyloFisher), written in Python 3. PhyloFisher includes a manually curated database of 240 protein-coding genes from 304 eukaryotic taxa covering known eukaryotic diversity, a novel tool for ortholog selection, and utilities that will perform diverse analyses required by state-of-the-art phylogenomic investigations. Through phylogenetic reconstructions of the tree of eukaryotes and of the Saccharomycetaceae clade of budding yeasts, we demonstrate the utility of the PhyloFisher workflow and the provided starting database to address phylogenetic questions across a large range of evolutionary time points for diverse groups of organisms. We also demonstrate that undetected paralogy can remain in phylogenomic "single-copy orthogroup" datasets constructed using widely accepted methods such as all vs. all BLAST searches followed by Markov Cluster Algorithm (MCL) clustering and application of automated tree pruning algorithms. Finally, we show how the PhyloFisher workflow helps detect inadvertent paralog inclusions, allowing the user to make more informed decisions regarding orthology assignments, leading to a more accurate final dataset.Alexander K TiceDavid ŽihalaTomáš PánekRobert E JonesEric D SalomakiSerafim NenarokovFabien BurkiMarek EliášLaura EmeAndrew J RogerAntonis RokasXing-Xing ShenJürgen F H StrassertMartin KolískoMatthew W BrownPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 19, Iss 8, p e3001365 (2021) |
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Biology (General) QH301-705.5 |
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Biology (General) QH301-705.5 Alexander K Tice David Žihala Tomáš Pánek Robert E Jones Eric D Salomaki Serafim Nenarokov Fabien Burki Marek Eliáš Laura Eme Andrew J Roger Antonis Rokas Xing-Xing Shen Jürgen F H Strassert Martin Kolísko Matthew W Brown PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. |
| description |
Phylogenomic analyses of hundreds of protein-coding genes aimed at resolving phylogenetic relationships is now a common practice. However, no software currently exists that includes tools for dataset construction and subsequent analysis with diverse validation strategies to assess robustness. Furthermore, there are no publicly available high-quality curated databases designed to assess deep (>100 million years) relationships in the tree of eukaryotes. To address these issues, we developed an easy-to-use software package, PhyloFisher (https://github.com/TheBrownLab/PhyloFisher), written in Python 3. PhyloFisher includes a manually curated database of 240 protein-coding genes from 304 eukaryotic taxa covering known eukaryotic diversity, a novel tool for ortholog selection, and utilities that will perform diverse analyses required by state-of-the-art phylogenomic investigations. Through phylogenetic reconstructions of the tree of eukaryotes and of the Saccharomycetaceae clade of budding yeasts, we demonstrate the utility of the PhyloFisher workflow and the provided starting database to address phylogenetic questions across a large range of evolutionary time points for diverse groups of organisms. We also demonstrate that undetected paralogy can remain in phylogenomic "single-copy orthogroup" datasets constructed using widely accepted methods such as all vs. all BLAST searches followed by Markov Cluster Algorithm (MCL) clustering and application of automated tree pruning algorithms. Finally, we show how the PhyloFisher workflow helps detect inadvertent paralog inclusions, allowing the user to make more informed decisions regarding orthology assignments, leading to a more accurate final dataset. |
| format |
article |
| author |
Alexander K Tice David Žihala Tomáš Pánek Robert E Jones Eric D Salomaki Serafim Nenarokov Fabien Burki Marek Eliáš Laura Eme Andrew J Roger Antonis Rokas Xing-Xing Shen Jürgen F H Strassert Martin Kolísko Matthew W Brown |
| author_facet |
Alexander K Tice David Žihala Tomáš Pánek Robert E Jones Eric D Salomaki Serafim Nenarokov Fabien Burki Marek Eliáš Laura Eme Andrew J Roger Antonis Rokas Xing-Xing Shen Jürgen F H Strassert Martin Kolísko Matthew W Brown |
| author_sort |
Alexander K Tice |
| title |
PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. |
| title_short |
PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. |
| title_full |
PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. |
| title_fullStr |
PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. |
| title_full_unstemmed |
PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. |
| title_sort |
phylofisher: a phylogenomic package for resolving eukaryotic relationships. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2021 |
| url |
https://doaj.org/article/5458e9e481234510ae6f912b55e8b0bb |
| work_keys_str_mv |
AT alexanderktice phylofisheraphylogenomicpackageforresolvingeukaryoticrelationships AT davidzihala phylofisheraphylogenomicpackageforresolvingeukaryoticrelationships AT tomaspanek phylofisheraphylogenomicpackageforresolvingeukaryoticrelationships AT robertejones phylofisheraphylogenomicpackageforresolvingeukaryoticrelationships AT ericdsalomaki phylofisheraphylogenomicpackageforresolvingeukaryoticrelationships AT serafimnenarokov phylofisheraphylogenomicpackageforresolvingeukaryoticrelationships AT fabienburki phylofisheraphylogenomicpackageforresolvingeukaryoticrelationships AT marekelias phylofisheraphylogenomicpackageforresolvingeukaryoticrelationships AT lauraeme phylofisheraphylogenomicpackageforresolvingeukaryoticrelationships AT andrewjroger phylofisheraphylogenomicpackageforresolvingeukaryoticrelationships AT antonisrokas phylofisheraphylogenomicpackageforresolvingeukaryoticrelationships AT xingxingshen phylofisheraphylogenomicpackageforresolvingeukaryoticrelationships AT jurgenfhstrassert phylofisheraphylogenomicpackageforresolvingeukaryoticrelationships AT martinkolisko phylofisheraphylogenomicpackageforresolvingeukaryoticrelationships AT matthewwbrown phylofisheraphylogenomicpackageforresolvingeukaryoticrelationships |
| _version_ |
1718375900050882560 |