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Zenodo
2025
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| On-line přístup: | https://doi.org/10.5281/zenodo.17791104 |
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| _version_ | 1866901652846411776 |
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| author | Terra, Rafael Carvalho, Diego Osthoff, Carla Ocaña, Kary |
| author_facet | Terra, Rafael Carvalho, Diego Osthoff, Carla Ocaña, Kary |
| contents | Phylogeny refers to the evolutionary history and relationship between biological lineages related by common descent. Reticulate evolution refers to the origination of lineages through the complete or partial merging of ancestor lineages. Networks may be used to represent lineage independence events in non-treelike phylogenetic processes. The methodology for reconstructing networks is still in development. Here we explore two methods for reconstructing rooted explicit phylogenetic networks, PhyloNetworks and Phylonet, which employ computationally expensive and time consuming algorithms. The construction of phylogenetic networks follows a coordinated processing flow of data sets analyzed and processed by the coordinated execution of a set of different programs, packages, libraries or pipelines, called workflow activities. In view of the complexity in modeling network experiments, the present work introduces a workflow for phylogenetic network analyses coupled to be executed in High-Performance Computing (HPC) environments. The workflow aims to integrate well-established software, pipelines and scripts, implementing a challenging task since these tools do not consistently profit from the HPC environment, leading to an increase in the expected makespan and idle computing resources. |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17791104 |
| institution | Zenodo |
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| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | HP2NET - High Performance Phylogenetic Network Terra, Rafael Carvalho, Diego Osthoff, Carla Ocaña, Kary Scientific Workflows Phylogenetic Networks High-Performance Computing Parsl Phylogeny refers to the evolutionary history and relationship between biological lineages related by common descent. Reticulate evolution refers to the origination of lineages through the complete or partial merging of ancestor lineages. Networks may be used to represent lineage independence events in non-treelike phylogenetic processes. The methodology for reconstructing networks is still in development. Here we explore two methods for reconstructing rooted explicit phylogenetic networks, PhyloNetworks and Phylonet, which employ computationally expensive and time consuming algorithms. The construction of phylogenetic networks follows a coordinated processing flow of data sets analyzed and processed by the coordinated execution of a set of different programs, packages, libraries or pipelines, called workflow activities. In view of the complexity in modeling network experiments, the present work introduces a workflow for phylogenetic network analyses coupled to be executed in High-Performance Computing (HPC) environments. The workflow aims to integrate well-established software, pipelines and scripts, implementing a challenging task since these tools do not consistently profit from the HPC environment, leading to an increase in the expected makespan and idle computing resources. |
| title | HP2NET - High Performance Phylogenetic Network |
| topic | Scientific Workflows Phylogenetic Networks High-Performance Computing Parsl |
| url | https://doi.org/10.5281/zenodo.17791104 |