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SonicParanoid: fast, accurate and easy orthology inference
2018
Bioinformatics
Preserved Fulltext
Supplementary Text
Orthology Inference in SonicParanoid SonicParanoid is a graph-based orthology inference tool. ...
Execution time and scalability of SonicParanoid in the inference of ortholog groups. ...
doi:10.1093/bioinformatics/bty631
pmid:30032301
fatcat:cmxmzps47vby5papmatr5q3foe
SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier
2019
GigaScience
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Findings Here we present a new graph-based orthology analysis tool, SwiftOrtho, which is optimized for speed and memory usage when applied to large-scale data. ...
Conclusions SwiftOrtho enables the accurate comparative genomic analyses of thousands of genomes using low-memory computers. SwiftOrtho is available at https://github.com/Rinoahu/SwiftOrtho ...
X.H. wrote the software and performed the analysis. Both authors wrote the manuscript.
Acknowledgments The authors acknowledge fruitful discussions with all members of the Friedberg Laboratory. ...
doi:10.1093/gigascience/giz118
pmid:31648300
pmcid:PMC6812468
fatcat:u4iudt64nzhitk6l7lxtcixcea
SwiftOrtho: a Fast, Memory-Efficient, Multiple Genome Orthology Classifier
[article]
2019
bioRxiv
pre-print
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To address this problem, we developed a new graph-based orthology analysis tool, SwiftOrtho,which is optimized for speed and memory usage when applied to large-scale data. ...
SwiftOrtho enables the accurate comparative genomic analyses of thousands of genomes using low memory computers. Availability: https://github.com/Rinoahu/SwiftOrtho ...
SwiftOrtho is not only fast 391 but also accurate, as showing the results produced when running on orthobench 392
summary, SwiftOrtho is a fast, accurate orthology prediction tool that can an-395 alyze ...
doi:10.1101/543223
fatcat:2n7hqfc4rzcr3haciqj4a3pebm
OrthoFinder: phylogenetic orthology inference for comparative genomics
2019
Genome Biology
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The file type is application/pdf.
Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. ...
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 ...
The orthologs inferred by all methods and all benchmark results are available from the Quest for Orthologs Benchmark Server [1] : https://orthology.benchmarkservice.org. ...
doi:10.1186/s13059-019-1832-y
pmid:31727128
pmcid:PMC6857279
fatcat:rokdco7onzgxnldxfigyrhowny
Phylogenetic profiling in eukaryotes: The effect of species, orthologous group, and interactome selection on protein interaction prediction
[article]
2021
bioRxiv
pre-print
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This interest is likely driven by the increased number of available diverse genomes and computational methods to infer orthologies. ...
As part of our recent comparison of orthology inference methods for eukaryotic genomes, we observed a surprisingly high performance for predicting interacting orthologous groups. ...
SonicParanoid: Fast, accurate and easy orthology 593 inference. Bioinformatics. 2018;35: 149-151. doi:10.1093/bioinformatics/bty631 576
recombination
repair
genes. ...
doi:10.1101/2021.05.05.442724
fatcat:qavficgm3bevhnvq56gvc3po6i
PanACoTA: a modular tool for massive microbial comparative genomics
2021
NAR Genomics and Bioinformatics
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annotate and then build their pangenome, several variants of core genomes, their alignments and a rapid but accurate phylogenetic tree. ...
While many programs building pangenomes have become available in the last few years, we have focused on a modular method, that tackles all the key steps of the process, from download to phylogenetic inference ...
help with Singularity, and Bertrand NERON for help on pypi and conda packages. ...
doi:10.1093/nargab/lqaa106
pmid:33575648
pmcid:PMC7803007
fatcat:4yq5ogs7gjhr3acck33rdc6rj4
PanACoTA: A modular tool for massive microbial comparative genomics
[article]
2020
bioRxiv
pre-print
Preserved Fulltext
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a pangenome, several variants of core or persistent genomes, their alignments, and a rapid but accurate phylogenetic tree. ...
The gene repertoires of microbial species, their pangenomes, evolve very fast. Their study facilitates the discrimination between lineages and reveals which genes drive their recent adaptation. ...
Acknowledgements We thank Marie TOUCHON, Matthieu HAUDIQUET and Rémi DENISE for comments, suggestions, and bug reports, Yoann DUFRESNE for his help on optimizing some parts of the code, and Blaise LI for ...
doi:10.1101/2020.09.11.293472
fatcat:gspt363dmva5vdzxt4irhsgj7q