ProtTest: selection of best-fit models of protein evolution

A Mathematical Theory of Communication

Shannon, C. E. (1948) · Bell System Technical Journal · doi:10.1002/j.1538-7305.1948.tb01338.x · Cited by 88,486 · see citing works

Estimating the Dimension of a Model

Schwarz, G. (1978) · The Annals of Statistics · doi:10.1214/aos/1176344136 · Cited by 47,033 · see citing works

Model selection and multimodel inference: a practical information-theoretic approach.

Guthery, F. S., Burnham, K. P., & Anderson, D. R. (2003) · The Journal of Wildlife Management · doi:10.2307/3802723 · Cited by 41,495 · see citing works

MODELTEST: testing the model of DNA substitution.

Posada, D., & Crandall, K. A. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.817 · Cited by 19,820 · see citing works

Information Theory and an Extension of the Maximum Likelihood Principle

Akaike, H. (1998) · Springer series in statistics · doi:10.1007/978-1-4612-1694-0_15 · Cited by 18,384 · see citing works

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

Guindon, S., & Gascuel, O. (2003) · Systematic Biology · doi:10.1080/10635150390235520 · Cited by 16,698 · see citing works

The rapid generation of mutation data matrices from protein sequences

Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992) · Computer applications in the biosciences · doi:10.1093/bioinformatics/8.3.275 · Cited by 6,916 · see citing works

Amino acid substitution matrices from protein blocks.

Henikoff, S., & Henikoff, J. G. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.22.10915 · Cited by 6,218 · see citing works

MacClade 4.0: analysis of phylogeny and character evolution

(2001) · Choice Reviews Online · doi:10.5860/choice.39-2183 · Cited by 5,533 · see citing works

Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests

Posada, D., & Buckley, T. R. (2004) · Systematic Biology · doi:10.1080/10635150490522304 · Cited by 3,927 · see citing works

A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach

Whelan, S., & Goldman, N. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003851 · Cited by 2,849 · see citing works

Further analysis of the data by Akaike's information criterion and the finite corrections

Sugiura, N. (1978) · Communication in Statistics- Theory and Methods · doi:10.1080/03610927808827599 · Cited by 2,148 · see citing works

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data

Gascuel, O. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025808 · Cited by 1,850 · see citing works

Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites.

Yang, Z. (1993) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040082 · Cited by 1,040 · see citing works

Model of Amino Acid Substitution in Proteins Encoded by Mitochondrial DNA

Adachi, J., & Hasegawa, M. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02498640 · Cited by 514 · see citing works

Modeling Amino Acid Replacement

Müller, T., & Vingron, M. (2000) · Journal of Computational Biology · doi:10.1089/10665270050514918 · Cited by 359 · see citing works

Plastid Genome Phylogeny and a Model of Amino Acid Substitution for Proteins Encoded by Chloroplast DNA

Adachi, J., Waddell, P. J., Martin, W. F., & Hasegawa, M. (2000) · Journal of Molecular Evolution · doi:10.1007/s002399910038 · Cited by 253 · see citing works

rtREV: An Amino Acid Substitution Matrix for Inference of Retrovirus and Reverse Transcriptase Phylogeny

Dimmic, M. W., Rest, J. S., Mindell, D. P., & Goldstein, R. A. (2002) · Journal of Molecular Evolution · doi:10.1007/s00239-001-2304-y · Cited by 244 · see citing works

Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene

Cao, Y., Adachi, J., Janke, A., P��bo, S., & Hasegawa, M. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00173421 · Cited by 244 · see citing works

Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders

Cao, Y., Janke, A., Waddell, P. J., Westerman, M., Takenaka, O., Murata, S., Okada, N., Pääbo, S., & Hasegawa, M. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006389 · Cited by 234 · see citing works

MtArt: A New Model of Amino Acid Replacement for Arthropoda

Abascal, F., Posada, D., & Zardoya, R. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl136 · Cited by 211 · see citing works

PAL: an object-oriented programming library for molecular evolution and phylogenetics

Drummond, A. J., & Strimmer, K. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.7.662 · Cited by 157 · see citing works

Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA

Reeves, J. H. (1992) · Journal of Molecular Evolution · doi:10.1007/bf00160257 · Cited by 147 · see citing works

Models of protein sequence evolution and their applications

Thorne, J. L. (2000) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(00)00142-8 · Cited by 81 · see citing works

Probabilistic Models for the Study of Protein Evolution

Thorne, J. L., & Goldman, N. (2007) · Wiley eBooks · doi:10.1002/9780470061619.ch14 · Cited by 9 · see citing works

ModelFinder: fast model selection for accurate phylogenetic estimates

Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., & Jermiin, L. S. (2017) · Nature Methods · doi:10.1038/nmeth.4285 · Cited by 18,449 · see citing works

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

King, N., Westbrook, M. J., Young, S. L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., et al. (2008) · Nature · doi:10.1038/nature06617 · Cited by 1,139 · see citing works

Improving the coverage of the cyanobacterial phylum using diversity driven genome sequencing

Shih, P. M., Wu, D., Latifi, A., Axen, S. D., Fewer, D. P., Talla, E., Calteau, A., Cai, F., Tandeau de Marsac, N., Rippka, R., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1217107110 · Cited by 800 · see citing works

Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors

Shah, F., Nicolás, C., Bentzer, J., Ellström, M., Smits, M., Rineau, F., Canbäck, B., Floudas, D., Carleer, R., Lackner, G., et al. (2016) · New Phytologist · doi:10.1111/nph.13722 · Cited by 394 · see citing works

Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

Feuda, R., Dohrmann, M., Pett, W., Philippe, H., Rota-Stabelli, O., Lartillot, N., Wörheide, G., & Pisani, D. (2017) · Current Biology · doi:10.1016/j.cub.2017.11.008 · Cited by 291 · see citing works

Auxin-related gene families in abiotic stress response in Sorghum bicolor

Wang, S., Bai, Y., Shen, C., Wu, Y., Zhang, S., Jiang, D., Guilfoyle, T. J., Chen, M., & Qi, Y. (2010) · Functional & Integrative Genomics · doi:10.1007/s10142-010-0174-3 · Cited by 297 · see citing works

A Post-Synaptic Scaffold at the Origin of the Animal Kingdom

Sakarya, O., Armstrong, K. A., Adamska, M., Adamski, M., Wang, I.-F., Tidor, B., Degnan, B. M., Oakley, T. H., & Kosik, K. S. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000506 · Cited by 291 · see citing works

Marine Tubeworm Metamorphosis Induced by Arrays of Bacterial Phage Tail–Like Structures

Shikuma, N. J., Pilhofer, M., Weiss, G. L., Hadfield, M. G., Jensen, G. J., & Newman, D. K. (2014) · Science · doi:10.1126/science.1246794 · Cited by 267 · see citing works

Deep metazoan phylogeny: When different genes tell different stories

Nosenko, T., Schreiber, F., Adamska, M., Adamski, M., Eitel, M., Hammel, J., Maldonado, M., Müller, W. E. G., Nickel, M., Schierwater, B., et al. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.01.010 · Cited by 254 · see citing works

Independent evolution of striated muscles in cnidarians and bilaterians

Steinmetz, P. R. H., Kraus, J. E. M., Larroux, C., Hammel, J. U., Amon-Hassenzahl, A., Houliston, E., Wörheide, G., Nickel, M., Degnan, B. M., & Technau, U. (2012) · Nature · doi:10.1038/nature11180 · Cited by 252 · see citing works

A formal test of the theory of universal common ancestry

Theobald, D. L. (2010) · Nature · doi:10.1038/nature09014 · Cited by 231 · see citing works

Biased gene transfer in microbial evolution

Andam, C. P., & Gogarten, J. P. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2593 · Cited by 172 · see citing works

A late methanogen origin for molybdenum-dependent nitrogenase

BOYD, E. S., ANBAR, A. D., MILLER, S., HAMILTON, T. L., LAVIN, M., & PETERS, J. W. (2011) · Geobiology · doi:10.1111/j.1472-4669.2011.00278.x · Cited by 161 · see citing works

Evolution of sodium channels predates the origin of nervous systems in animals

Liebeskind, B. J., Hillis, D. M., & Zakon, H. H. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1106363108 · Cited by 149 · see citing works

Stress-induced accumulation of DcAOX1 and DcAOX2a transcripts coincides with critical time point for structural biomass prediction in carrot primary cultures (Daucus carota L.).

Campos, M. D., Nogales, A., Cardoso, H. G., Kumar, S. R., Nobre, T., Sathishkumar, R., & Arnholdt-Schmitt, B. (2016) · Frontiers in Genetics · doi:10.3389/fgene.2016.00001 · Cited by 152 · see citing works

Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins

Shih, P. M., & Matzke, N. J. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1305813110 · Cited by 151 · see citing works

KLF/SP Transcription Factor Family Evolution: Expansion, Diversification, and Innovation in Eukaryotes

Presnell, J. S., Schnitzler, C. E., & Browne, W. E. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv141 · Cited by 119 · see citing works

Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes

Schnitzler, C. E., Pang, K., Powers, M. L., Reitzel, A. M., Ryan, J. F., Simmons, D., Tada, T., Park, M., Gupta, J., Brooks, S. Y., et al. (2012) · BMC Biology · doi:10.1186/1741-7007-10-107 · Cited by 132 · see citing works

Mycobacterial Pan-Genome Analysis Suggests Important Role of Plasmids in the Radiation of Type VII Secretion Systems

Dumas, E., Christina Boritsch, E., Vandenbogaert, M., Rodríguez de la Vega, R. C., Thiberge, J.-M., Caro, V., Gaillard, J.-L., Heym, B., Girard-Misguich, F., Brosch, R., et al. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw001 · Cited by 112 · see citing works

A key role for the peroxisomal<i>ABCD2</i>transporter in fatty acid homeostasis

Fourcade, S., Ruiz, M., Camps, C., Schlüter, A., Houten, S. M., Mooyer, P. A. W., Pàmpols, T., Dacremont, G., Wanders, R. J. A., Giròs, M., et al. (2009) · American Journal of Physiology-Endocrinology and Metabolism · doi:10.1152/ajpendo.90736.2008 · Cited by 104 · see citing works

What RNA World? Why a Peptide/RNA Partnership Merits Renewed Experimental Attention

Carter, C. (2015) · Life · doi:10.3390/life5010294 · Cited by 95 · see citing works

Differential evolution of voltage-gated sodium channels in tetrapods and teleost fishes

Widmark, J., Sundstrom, G., Ocampo Daza, D., & Larhammar, D. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msq257 · Cited by 88 · see citing works

The cryptochrome/photolyase family in aquatic organisms

Oliveri, P., Fortunato, A. E., Petrone, L., Ishikawa-Fujiwara, T., Kobayashi, Y., Todo, T., Antonova, O., Arboleda, E., Zantke, J., Tessmar-Raible, K., et al. (2014) · Marine Genomics · doi:10.1016/j.margen.2014.02.001 · Cited by 90 · see citing works

The Tissue-Specific RNA Binding Protein T-STAR Controls Regional Splicing Patterns of Neurexin Pre-mRNAs in the Brain

Ehrmann, I., Dalgliesh, C., Liu, Y., Danilenko, M., Crosier, M., Overman, L., Arthur, H. M., Lindsay, S., Clowry, G. J., Venables, J. P., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003474 · Cited by 82 · see citing works

Convergent Evolution of Sodium Ion Selectivity in Metazoan Neuronal Signaling

Gur Barzilai, M., Reitzel, A. M., Kraus, J. E. M., Gordon, D., Technau, U., Gurevitz, M., & Moran, Y. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.06.016 · Cited by 76 · see citing works

New genomic data and analyses challenge the traditional vision of animal epithelium evolution

Belahbib, H., Renard, E., Santini, S., Jourda, C., Claverie, J.-M., Borchiellini, C., & Le Bivic, A. (2018) · BMC Genomics · doi:10.1186/s12864-018-4715-9 · Cited by 71 · see citing works

Diversity and evolution of myxozoan minicollagens and nematogalectins

Shpirer, E., Chang, E. S., Diamant, A., Rubinstein, N., Cartwright, P., & Huchon, D. (2014) · BMC Evolutionary Biology · doi:10.1186/s12862-014-0205-0 · Cited by 63 · see citing works

Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life

Hoeppner, M. P., Gardner, P. P., & Poole, A. M. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002752 · Cited by 62 · see citing works

Peroxisomes, myelination, and axonal integrity in the CNS

Baes, M., & Aubourg, P. (2009) · The Neuroscientist · doi:10.1177/1073858409336297 · Cited by 65 · see citing works

On the phylogenetic position of Myzostomida: Can 77 genes get it wrong?

Bleidorn, C., Podsiadlowski, L., Zhong, M., Eeckhaut, I., Hartmann, S., Halanych, K. M., & Tiedemann, R. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-150 · Cited by 59 · see citing works

A family of diatom-like silicon transporters in the siliceous loricate choanoflagellates

Marron, A. O., Alston, M. J., Heavens, D., Akam, M., Caccamo, M., Holland, P. W. H., & Walker, G. (2013) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2012.2543 · Cited by 54 · see citing works

Plastid establishment did not require a chlamydial partner

Domman, D., Horn, M., Embley, T. M., & Williams, T. A. (2015) · Nature Communications · doi:10.1038/ncomms7421 · Cited by 51 · see citing works

Staphylococcus lugdunensis IsdG Liberates Iron from Host Heme

Haley, K. P., Janson, E. M., Heilbronner, S., Foster, T. J., & Skaar, E. P. (2011) · Journal of Bacteriology · doi:10.1128/jb.00436-11 · Cited by 53 · see citing works

Expression and phylogenetic analysis of the zic gene family in the evolution and development of metazoans

Layden, M. J., Meyer, N. P., Pang, K., Seaver, E. C., & Martindale, M. Q. (2010) · EvoDevo · doi:10.1186/2041-9139-1-12 · Cited by 46 · see citing works

Structural and evolutionary analyses reveal determinants of DNA binding specificities of nucleoid-associated proteins HU and IHF

Dey, D., Nagaraja, V., & Ramakumar, S. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.11.014 · Cited by 46 · see citing works

A genome-wide analysis of annexins from parasitic organisms and their vectors

Cantacessi, C., Seddon, J. M., Miller, T. L., Leow, C. Y., Thomas, L., Mason, L., Willis, C., Walker, G., Loukas, A., Gasser, R. B., et al. (2013) · Scientific Reports · doi:10.1038/srep02893 · Cited by 46 · see citing works

Lim homeobox genes in the Ctenophore Mnemiopsis leidyi: the evolution of neural cell type specification

Simmons, D. K., Pang, K., & Martindale, M. Q. (2012) · EvoDevo · doi:10.1186/2041-9139-3-2 · Cited by 38 · see citing works

Interrelationships of chromalveolates within a broadly sampled tree of photosynthetic protists

Reeb, V. C., Peglar, M. T., Yoon, H. S., Bai, J. R., Wu, M., Shiu, P., Grafenberg, J. L., Reyes-Prieto, A., Rümmele, S. E., & Gross, J. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.04.012 · Cited by 35 · see citing works

Subspecies-level genome comparison of Lactobacillus delbrueckii

Baek, M.-G., Kim, K. W., & Yi, H. (2023) · Scientific Reports · doi:10.1038/s41598-023-29404-3 · Cited by 35 · see citing works

The <i> <scp>L</scp> egionella pneumophila kai </i> operon is implicated in stress response and confers fitness in competitive environments

Loza‐Correa, M., Sahr, T., Rolando, M., Daniels, C., Petit, P., Skarina, T., Gomez Valero, L., Dervins‐Ravault, D., Honoré, N., Savchenko, A., et al. (2014) · Environmental Microbiology · doi:10.1111/1462-2920.12223 · Cited by 34 · see citing works

On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence

Theobald, D. L. (2011) · Biology Direct · doi:10.1186/1745-6150-6-60 · Cited by 16 · see citing works

Molecular Basis for the Evolution of Species-Specific Hemoglobin Capture by Staphylococcus aureus

Choby, J. E., Buechi, H. B., Farrand, A. J., Skaar, E. P., & Barber, M. F. (2018) · mBio · doi:10.1128/mbio.01524-18 · Cited by 15 · see citing works

Conservation of three-dimensional helix-loop-helix structure through the vertebrate lineage reopens the cold case of gonadotropin-releasing hormone-associated Peptide

Pérez Sirkin, D. I., Lafont, A.-G., Kamech, N., Somoza, G. M., Vissio, P. G., & Dufour, S. (2017) · Frontiers in Endocrinology · doi:10.3389/fendo.2017.00207 · Cited by 14 · see citing works

Susquehanna Chorale Spring Concert "Roots and Wings"

Hawkins, D. (2017)

Using DataGrid Control to Realize DataBase of Querying in VB6.0

Hu, S. (2000) · Modern Computer

Study and Two Types of Typical Usage of DataGrid Web Server Control

Hai-tao, L. (2005) · Modern Computer

Achieving Parameter of DBSCAN Based on Datagrid

Xu, Q. (2010)

PACWON: A parallelizing compiler for workstations on a network

Das, D. K., & Das, P. P. (1998) · Journal of Systems Architecture · doi:10.1016/s1383-7621(97)00078-7