We are analyzing https://link.springer.com/article/10.1186/s13059-019-1832-y.

Title:
OrthoFinder: phylogenetic orthology inference for comparative genomics | Genome Biology
Description:
Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics. Each output is benchmarked on appropriate real or simulated datasets, and where comparable methods exist, OrthoFinder is equivalent to or outperforms these methods. Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. Finally, OrthoFinder’s comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. OrthoFinder is available at https://github.com/davidemms/OrthoFinder .
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Keywords {🔍}

species, gene, tree, orthofinder, trees, inference, methods, orthologs, method, duplication, genes, set, pubmed, article, orthogroup, sequence, google, scholar, phylogenetic, ortholog, analysis, events, rooted, sets, fig, cas, accuracy, orthology, complete, data, algorithm, additional, accurate, node, multiple, inferred, dataset, file, search, dlcpar, central, event, datasets, default, bipartition, full, orthogroups, root, outgroup, number,

Topics {✒️}

default version f-score/pseudo-f-score higher f-score/pseudo-f-score uk/pub/databases/reference_proteomes/previous_releases/ real-world large-scale analyses estimating maximum-likelihood phylogenies similarity score-based estimates comparative genomics statistics higher pseudo-f-score central premise underlying command-line power tool }_{ad}=\frac{\mid score-based heuristic method article download pdf score-based heuristic methods }_{io}=\frac{\left user-editable configuration file article emms pairwise species comparisons sensitive protein alignment tree-based online databases �pseudo-f-score” comparative biological research post-order traversal enables duplication-loss-coalescent model duplication-loss-coalescent model [32] multiple sequence alignment score-based estimates incomplete lineage sorting privacy choices/manage cookies duplication-loss-coalescent algorithm genome orthology inference thompson jd comparative genomics sequence similarity searches robinson-foulds distance multiple sequence alignments super-linear scaling normalized robinson-foulds creative commons license genome-scale coestimation duplication f-score bipartition correctly includes/excludes huerta-cepas genes observed post-duplication molecular biology large-scale analysis required f-score measures related subjects ground truth data tree inference error

Schema {🗺️}

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         description:Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics. Each output is benchmarked on appropriate real or simulated datasets, and where comparable methods exist, OrthoFinder is equivalent to or outperforms these methods. Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. Finally, OrthoFinder’s comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. OrthoFinder is available at https://github.com/davidemms/OrthoFinder .
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            Gene tree inference
            Gene duplication
            Comparative genomics
            Animal Genetics and Genomics
            Human Genetics
            Plant Genetics and Genomics
            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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      headline:OrthoFinder: phylogenetic orthology inference for comparative genomics
      description:Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics. Each output is benchmarked on appropriate real or simulated datasets, and where comparable methods exist, OrthoFinder is equivalent to or outperforms these methods. Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. Finally, OrthoFinder’s comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. OrthoFinder is available at https://github.com/davidemms/OrthoFinder .
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         Ortholog inference
         Gene tree inference
         Gene duplication
         Comparative genomics
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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