OrthoFinder: phylogenetic orthology inference for comparative genomics

[1]  Wataru Iwasaki,et al.  SonicParanoid: fast, accurate and easy orthology inference , 2018, Bioinform..

[2]  S. Kelly,et al.  OrthoFinder2: fast and accurate phylogenomic orthology analysis from gene sequences , 2018, bioRxiv.

[3]  David Sankoff,et al.  Accurate prediction of orthologs in the presence of divergence after duplication , 2018, bioRxiv.

[4]  S. Kelly,et al.  STAG: Species Tree Inference from All Genes , 2018, bioRxiv.

[5]  Jeroniza Nunes Marchaukoski,et al.  New Tools in Orthology Analysis: A Brief Review of Promising Perspectives , 2017, Front. Genet..

[6]  Johannes Söding,et al.  MMseqs2: sensitive protein sequence searching for the analysis of massive data sets , 2017, bioRxiv.

[7]  Ioannis Xenarios,et al.  Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree , 2017, bioRxiv.

[8]  Antonis Rokas,et al.  Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets , 2017, bioRxiv.

[9]  S. Kelly,et al.  STRIDE: Species Tree Root Inference from Gene Duplication Events , 2017, bioRxiv.

[10]  Albert J. Vilella,et al.  Ensembl comparative genomics resources , 2016, Database J. Biol. Databases Curation.

[11]  Adrian M. Altenhoff,et al.  Standardized benchmarking in the quest for orthologs , 2016, Nature Methods.

[12]  P. Bork,et al.  ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data , 2016, Molecular biology and evolution.

[13]  Albert J. Vilella,et al.  Ensembl comparative genomics resources , 2016, Database : the journal of biological databases and curation.

[14]  S. Kelly,et al.  OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy , 2015, Genome Biology.

[15]  Olivier Gascuel,et al.  FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program , 2015, Molecular biology and evolution.

[16]  Tandy J. Warnow,et al.  ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes , 2015, Bioinform..

[17]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[18]  Alessandro Vullo,et al.  Ensembl 2015 , 2014, Nucleic Acids Res..

[19]  Alessandro Vullo,et al.  The Ensembl REST API: Ensembl Data for Any Language , 2014, Bioinform..

[20]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[21]  Mukul S. Bansal,et al.  Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees , 2014, Genome research.

[22]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[23]  Damian Szklarczyk,et al.  eggNOG v4.0: nested orthology inference across 3686 organisms , 2013, Nucleic Acids Res..

[24]  Salvador Capella-Gutiérrez,et al.  PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome , 2013, Nucleic Acids Res..

[25]  C. Dessimoz,et al.  Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals , 2013, Genome biology and evolution.

[26]  Fabian Schreiber,et al.  Hieranoid: hierarchical orthology inference. , 2013, Journal of molecular biology.

[27]  Antonis Rokas,et al.  Inferring ancient divergences requires genes with strong phylogenetic signals , 2013, Nature.

[28]  P. Maini,et al.  DendroBLAST: Approximate Phylogenetic Trees in the Absence of Multiple Sequence Alignments , 2013, PloS one.

[29]  M. Gouy,et al.  Genome-scale coestimation of species and gene trees , 2013, Genome research.

[30]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[31]  Liang Liu,et al.  Estimating species trees from unrooted gene trees. , 2011, Systematic biology.

[32]  P. Bork,et al.  Orthology prediction methods: A quality assessment using curated protein families , 2011, BioEssays : news and reviews in molecular, cellular and developmental biology.

[33]  Arcady R. Mushegian,et al.  Computational methods for Gene Orthology inference , 2011, Briefings Bioinform..

[34]  Olivier Poch,et al.  A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives , 2011, PloS one.

[35]  Gaston H. Gonnet,et al.  OMA 2011: orthology inference among 1000 complete genomes , 2010, Nucleic Acids Res..

[36]  Ole Tange,et al.  GNU Parallel: The Command-Line Power Tool , 2011, login Usenix Mag..

[37]  Olivier Poch,et al.  OrthoInspector: comprehensive orthology analysis and visual exploration , 2011, BMC Bioinformatics.

[38]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[39]  Erik L. L. Sonnhammer,et al.  InParanoid 7: new algorithms and tools for eukaryotic orthology analysis , 2009, Nucleic Acids Res..

[40]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[41]  J. Dopazo,et al.  The human phylome , 2007, Genome Biology.

[42]  Tao Liu,et al.  TreeFam: a curated database of phylogenetic trees of animal gene families , 2005, Nucleic Acids Res..

[43]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[44]  Christian E. V. Storm,et al.  Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. , 2001, Journal of molecular biology.

[45]  Sean R. Eddy,et al.  A simple algorithm to infer gene duplication and speciation events on a gene tree , 2001, Bioinform..

[46]  Dannie Durand,et al.  NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees , 2000, J. Comput. Biol..

[47]  W. Fitch.  Distinguishing homologous from analogous proteins. , 1970, Systematic zoology.