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SonicParanoid: fast, accurate and easy orthology inference

Salvatore Cosentino, Wataru Iwasaki, Russell Schwartz
2018 Bioinformatics  
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

Xiao Hu, Iddo Friedberg
2019 GigaScience  
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]

Xiao Hu, Iddo Friedberg
2019 bioRxiv   pre-print
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

David M. Emms, Steven Kelly
2019 Genome Biology  
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]

Eva S. Deutekom, Teunis J.P. van Dam, Berend Snel
2021 bioRxiv   pre-print
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

Amandine Perrin, Eduardo P C Rocha
2021 NAR Genomics and Bioinformatics  
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]

Amandine PERRIN, Eduardo ROCHA
2020 bioRxiv   pre-print
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