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Journal articles on the topic 'Phylogenetics'

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Published: 4 June 2021
Last updated: 6 September 2023

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1

Wiley, E. "Phylogenetics." Scholarpedia 3, no. 12 (2008): 6299. http://dx.doi.org/10.4249/scholarpedia.6299.

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2

Sleator, Roy D. "Phylogenetics." Archives of Microbiology 193, no. 4 (January 20, 2011): 235–39. http://dx.doi.org/10.1007/s00203-011-0677-x.

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3

Talianová, M. "Survey of molecular phylogenetics." Plant, Soil and Environment 53, No. 9 (January 7, 2008): 413–16. http://dx.doi.org/10.17221/2290-pse.

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Rapidly increasing amount of biological data necessarily requires techniques that would enable to extract the information hidden in the data. Methods of molecular phylogenetics are commonly used tools as well as objects of continuous research within many fields, such as evolutionary biology, systematics, epidemiology, genomics, etc. The evolutionary process not only determines relationships among species, but also allows prediction of structural, physiological and biochemical properties of biomolecules. The article provides the reader with a brief overview of common methods that are currently employed in the field of molecular phylogenetics.
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4

Rothfels, Carl J. "Polyploid phylogenetics." New Phytologist 230, no. 1 (January 25, 2021): 66–72. http://dx.doi.org/10.1111/nph.17105.

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5

Sanderson, Michael J., and Junhyong Kim. "Parametric Phylogenetics?" Systematic Biology 49, no. 4 (December 1, 2000): 817–29. http://dx.doi.org/10.1080/106351500750049860.

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6

Pillay, Deenan, Andrew Rambaut, Anna Maria Geretti, and Andrew J. Leigh Brown. "HIV phylogenetics." BMJ 335, no. 7618 (September 6, 2007): 460–61. http://dx.doi.org/10.1136/bmj.39315.398843.be.

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7

McCabe, Declan J. "Competitive Phylogenetics." American Biology Teacher 76, no. 2 (February 1, 2014): 127–31. http://dx.doi.org/10.1525/abt.2014.76.2.10.

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This exercise demonstrates the principle of parsimony in constructing cladograms. Although it is designed using mammalian cranial characters, the activity could be adapted for characters from any group of organisms. Students score categorical traits on skulls and record the data in a spreadsheet. Using the Mesquite software package, students generate arbitrary cladograms and measure tree length. They then move taxa around to reduce tree length. The exercise can become competitive when students report out on tree lengths and try to achieve shorter trees than their peers. The resulting cladograms can be compared with a published mammalian phylogeny. The exercise illustrates phylogenetics, the principle of parsimony, and hypothesis testing using morphological data.
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8

Bowern, Claire. "Computational Phylogenetics." Annual Review of Linguistics 4, no. 1 (January 14, 2018): 281–96. http://dx.doi.org/10.1146/annurev-linguistics-011516-034142.

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9

Jofré, Paula, and Payel Das. "Galactic Phylogenetics." Proceedings of the International Astronomical Union 13, S334 (July 2017): 308–9. http://dx.doi.org/10.1017/s1743921317010791.

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AbstractPhylogenetics is a widely used concept in evolutionary biology. It is the reconstruction of evolutionary history by building trees that represent branching patterns and sequences. These trees represent shared history, and it is our contention that this approach can be employed in the analysis of Galactic history. In Galactic archaeology the shared environment is the interstellar medium in which stars form and provides the basis for tree-building as a methodological tool. Using elemental abundances of solar-type stars as a proxy for DNA, we built such an evolutionary tree to study the chemical evolution of the solar neighbourhood and published in Jofré15 et al. (2017). In this proceeding we summarise these results and discuss future prospects.
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10

Lowenstein, J. M. "Molecular Phylogenetics." Annual Review of Earth and Planetary Sciences 14, no. 1 (May 1986): 71–83. http://dx.doi.org/10.1146/annurev.ea.14.050186.000443.

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11

Peng, Wayne. "Tumor phylogenetics." Nature Genetics 44, no. 4 (March 28, 2012): 368. http://dx.doi.org/10.1038/ng.2240.

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12

Liu, Guo-Qing, Lian Lian, and Wei Wang. "The Molecular Phylogeny of Land Plants: Progress and Future Prospects." Diversity 14, no. 10 (September 21, 2022): 782. http://dx.doi.org/10.3390/d14100782.

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Phylogenetics has become a powerful tool in many areas of biology. Land plants are the most important primary producers of terrestrial ecosystems and have colonized various habitats on Earth. In the past two decades, tremendous progress has been made in our understanding of phylogenetic relationships at all taxonomic levels across all land plant groups by employing DNA sequence data. Here, we review the progress made in large-scale phylogenetic reconstructions of land plants and assess the current situation of phylogenetic studies of land plants. We then emphasize directions for future study. At present, the phylogenetic framework of land plants at the order and familial levels has been well built. Problematic deep-level relationships within land plants have also been well resolved by phylogenomic analyses. We pointed out five major aspects of molecular phylogenetics of land plants, which are nowadays being studied and will continue to be goals moving forward. These five aspects include: (1) constructing the genus- and species-level phylogenies for land plant groups, (2) updating the classification systems by combining morphological and molecular data, (3) integrating fossil taxa into phylogenies derived from living taxa, (4) resolving deep-level and/or rapidly divergent phylogenetic relationships using phylogenomic data, and (5) building big trees using the supermatrix method. We hope that this review paper will promote the development of plant molecular phylogenetics and other related areas.
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13

Zhang, Xiaorong. "Teaching molecular phylogenetics through investigating a real-world phylogenetic problem." Journal of Biological Education 46, no. 2 (June 2012): 103–9. http://dx.doi.org/10.1080/00219266.2011.634018.

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14

Duarte, Leandro D. S., Vanderlei J. Debastiani, André V. L. Freitas, and Valério D. Pillar. "Dissecting phylogenetic fuzzy weighting: theory and application in metacommunity phylogenetics." Methods in Ecology and Evolution 7, no. 8 (March 10, 2016): 937–46. http://dx.doi.org/10.1111/2041-210x.12547.

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15

Agorreta, Ainhoa, Diego San Mauro, Ulrich Schliewen, James L. Van Tassell, Marcelo Kovačić, Rafael Zardoya, and Lukas Rüber. "Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies." Molecular Phylogenetics and Evolution 69, no. 3 (December 2013): 619–33. http://dx.doi.org/10.1016/j.ympev.2013.07.017.

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16

Ash, Caroline. "Phylogenetics of superspreading." Science 371, no. 6529 (February 4, 2021): 580.15–582. http://dx.doi.org/10.1126/science.371.6529.580-o.

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17

Fay, Michael, Mark Chase, Nina Rønsted, Dion Devey, Yohan Pillon, Chris Pires, Gitte Peterson, Ole Seberg, and Jerrold Davis. "Phylogenetics of Lilliales." Aliso 22, no. 1 (2006): 599–65. http://dx.doi.org/10.5642/aliso.20062201.43.

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18

Berggren, Matz S. "Decapod crustacean phylogenetics." Marine Biology Research 6, no. 2 (March 2010): 221–22. http://dx.doi.org/10.1080/17451001003604796.

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19

Velasco, Joel D. "Philosophy and Phylogenetics." Philosophy Compass 8, no. 10 (October 2013): 990–98. http://dx.doi.org/10.1111/phc3.12070.

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20

Lyubetsky, Vassily, William H. Piel, and Peter F. Stadler. "Molecular Phylogenetics 2016." BioMed Research International 2016 (2016): 1–2. http://dx.doi.org/10.1155/2016/9029306.

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21

Long, Jeffrey C. "Human Molecular Phylogenetics." Annual Review of Anthropology 22, no. 1 (October 1993): 251–72. http://dx.doi.org/10.1146/annurev.an.22.100193.001343.

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22

Huson, Daniel H., Vincent Moulton, and Mike Steel. "Special Section: Phylogenetics." IEEE/ACM Transactions on Computational Biology and Bioinformatics 6, no. 1 (January 2009): 4–6. http://dx.doi.org/10.1109/tcbb.2009.21.

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23

Avni, Eliran, Reuven Cohen, and Sagi Snir. "Weighted Quartets Phylogenetics." Systematic Biology 64, no. 2 (November 19, 2014): 233–42. http://dx.doi.org/10.1093/sysbio/syu087.

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24

Ortiz-García, Sol, David S. Gernandt, Jeffrey K. Stone, Peter R. Johnston, Ignacio H. Chapela, Rodolfo Salas-Lizana, and Elena R. Alvarez-Buylla. "Phylogenetics ofLophodermiumfrom pine." Mycologia 95, no. 5 (September 2003): 846–59. http://dx.doi.org/10.1080/15572536.2004.11833044.

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25

Oxelman, Bengt, Anne Krag Brysting, Graham R. Jones, Thomas Marcussen, Christoph Oberprieler, and Bernard E. Pfeil. "Phylogenetics of Allopolyploids." Annual Review of Ecology, Evolution, and Systematics 48, no. 1 (November 2, 2017): 543–57. http://dx.doi.org/10.1146/annurev-ecolsys-110316-022729.

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26

Barraclough, Timothy G., and Sean Nee. "Phylogenetics and speciation." Trends in Ecology & Evolution 16, no. 7 (July 2001): 391–99. http://dx.doi.org/10.1016/s0169-5347(01)02161-9.

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27

Hillis, David M., John P. Huelsenbeck, and David L. Swofford. "Hobgoblin of phylogenetics?" Nature 369, no. 6479 (June 1994): 363–64. http://dx.doi.org/10.1038/369363a0.

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28

Lyubetsky, Vassily, William H. Piel, and Peter F. Stadler. "Molecular Phylogenetics 2014." BioMed Research International 2015 (2015): 1–2. http://dx.doi.org/10.1155/2015/919251.

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29

Retzlaff, Nancy, and Peter F. Stadler. "Phylogenetics beyond biology." Theory in Biosciences 137, no. 2 (June 21, 2018): 133–43. http://dx.doi.org/10.1007/s12064-018-0264-7.

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30

Laurin, Michel. "Systematics beyond phylogenetics." Comptes Rendus Palevol 12, no. 6 (August 2013): 327–31. http://dx.doi.org/10.1016/j.crpv.2013.09.001.

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31

Brooks, Daniel R., Richard L. Mayden, and Deborah A. McLennan. "Phylogenetics and conservation." Trends in Ecology & Evolution 7, no. 10 (October 1992): 353. http://dx.doi.org/10.1016/0169-5347(92)90132-u.

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32

Epstein, V. M. "The version of the contemporary theory of evolutionary systematics." Species and speciation. Analysis of new views and trends 313, Supplement 1 (July 25, 2009): 272–93. http://dx.doi.org/10.31610/trudyzin/2009.supl.1.272.

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Integral theory of evolutional systematics is presented in this article for the first time in contemporary science. It became formed as the science about evolution of species’ diversity and methods of investigation of it. Here is defined its object, subject, aim and method. Theoretical evolutional systematics is separated from practical systematics. Three sections are included in its content: idiographical systematics, nomothetical systematics and phylogenetical cybernetics. Idiographical systematics includes theories of descriptions (= meronomy), classifications (= taxonomy) and reconstructions of phylogenesis (= phylonomy). Nomothetical systematics includes the laws of phylogenetics, postulates of systematics, axioms and theorems of evolutional systematics in a whole, forming deductive theoretical system of evolutional systematics (DTS ES). Status of laws is added to 21 conformities to natural laws of phylogenetics. Here are formulated 6 postulates of systematics. On the base of logical investigations of laws and postulates as statements, the laws of phylogenetics are represented in form of 6 axioms and 15 theorems. Postulates of systematics are considered as 6 axioms. DTS ES is represented in the paper on the base of analysis of connections between 12 axioms. Phylogenetical cybernetics includes interpretation of the theory on the some systemic and probabilistic models of species, their classification and reconstruction of phylogenesis, the examples are present in the article. It is divided on three sections of investigations : systemology, theory of control phylogenetical transformations and theory of information processes in phylogenesis. The sections of evolutional systematics are interpreted accordingly philosophical conception of the levels of scientific knowledge. Systematics and phylogenetics are considered as two aspects of evolutional systematics as united science, reflecting its onthology (= the laws of phylogenesis) and gnosiologyl (= postulates of systematics). This solution conforms to initial definition of evolutional systematics as the science of evolution of species’ diversity and methods of its investigation and conforms the contemporary darwinism.
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33

Xia, Xuhua. "Imputing missing distances in molecular phylogenetics." PeerJ 6 (July 24, 2018): e5321. http://dx.doi.org/10.7717/peerj.5321.

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Missing data are frequently encountered in molecular phylogenetics, but there has been no accurate distance imputation method available for distance-based phylogenetic reconstruction. The general framework for distance imputation is to explore tree space and distance values to find an optimal combination of output tree and imputed distances. Here I develop a least-square method coupled with multivariate optimization to impute multiple missing distance in a distance matrix or from a set of aligned sequences with missing genes so that some sequences share no homologous sites (whose distances therefore need to be imputed). I show that phylogenetic trees can be inferred from distance matrices with about 10% of distances missing, and the accuracy of the resulting phylogenetic tree is almost as good as the tree from full information. The new method has the advantage over a recently published one in that it does not assume a molecular clock and is more accurate (comparable to maximum likelihood method based on simulated sequences). I have implemented the function in DAMBE software, which is freely available athttp://dambe.bio.uottawa.ca.
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34

David, Andrew A. "Using Project-Based Learning to Teach Phylogenetic Reconstruction for Advanced Undergraduate Biology Students: Molluscan Evolution as a Case Study." American Biology Teacher 80, no. 4 (April 1, 2018): 278–84. http://dx.doi.org/10.1525/abt.2018.80.4.278.

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Phylogenetics plays a central role in understanding the evolution of life on Earth, and as a consequence, several active teaching strategies have been employed to aid students in grasping basic phylogenetic principles. Although many of these strategies have been designed to actively engage undergraduate biology students at the freshman level, less attention is given to designing challenges for advanced students. Here, I present a project-based learning (PBL) activity that was developed to teach phylogenetics for junior and senior-level biology students. This approach reinforces the theories and concepts that students have learned in their freshman courses along with incorporating Bioinformatics, which is essential for teaching zoology in the 21st century.
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35

SUKPRASERT, APISAK, SURAPOP SUTTHIWISES, VIRAYUTH LAUHACHINDA, and WUT TAKSINTUM. "Two new species of Hemiphyllodactylus Bleeker (Squamata: Gekkonidae) from Thailand." Zootaxa 4369, no. 3 (January 5, 2018): 363. http://dx.doi.org/10.11646/zootaxa.4369.3.4.

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We investigate the taxonomy of slender geckos (Hemiphyllodactylus) in Thailand by means of molecular phylogenetics and morphological study using specimens from three provinces; Chiang Mai, Kamphaeng Phet, and Chanthaburi. The results of phylogenetic analyses had shown that the genetic data of populations from 2 provinces were distinctly different from known species. In addition, some morphological characters of these two populations such as lamellar formula on fore- and hindfoot differed from the other species. The integrated taxonomy using molecular phylogenetics and morphological study revealed two new species, Hemiphyllodactylus khlonglanensis sp. nov. from western Thailand, and Hemiphyllodactylus flaviventris sp. nov. from eastern Thailand as described herein.
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36

Matveeva, Tatyana V., Olga A. Pavlova, Denis I. Bogomaz, Andrey E. Demkovich, and Ludmila A. Lutova. "Molecular markers for plant species identification and phylogenetics." Ecological genetics 9, no. 1 (March 15, 2011): 32–43. http://dx.doi.org/10.17816/ecogen9132-43.

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In this review we summarized the information on application of molecular markers for plant species identification and phylogenetics: positive sides and limitations of main markers, representing sequencing data of taxonomically important chloroplast and nuclear DNA regions. Markers, based on polymorphism of PCR and restriction products, are also discussed as accessorial markers in phylogenetic studies.
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37

Marchán, Daniel Fernández, Thibaud Decaëns, Jorge Domínguez, and Marta Novo. "Perspectives in Earthworm Molecular Phylogeny: Recent Advances in Lumbricoidea and Standing Questions." Diversity 14, no. 1 (January 4, 2022): 30. http://dx.doi.org/10.3390/d14010030.

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Earthworm systematics have been limited by the small number of taxonomically informative morphological characters and high levels of homoplasy in this group. However, molecular phylogenetic techniques have yielded significant improvements in earthworm taxonomy in the last 15 years. Several different approaches based on the use of different molecular markers, sequencing techniques, and compromises between specimen/taxon coverage and phylogenetic information have recently emerged (DNA barcoding, multigene phylogenetics, mitochondrial genome analysis, transcriptome analysis, targeted enrichment methods, and reduced representation techniques), providing solutions to different evolutionary questions regarding European earthworms. Molecular phylogenetics have led to significant advances being made in Lumbricidae systematics, such as the redefinition or discovery of new genera (Galiciandrilus, Compostelandrilus, Vindoboscolex, Castellodrilus), delimitation and revision of previously existing genera (Kritodrilus, Eophila, Zophoscolex, Bimastos), and changes to the status of subspecific taxa (such as the Allolobophorachaetophora complex). These approaches have enabled the identification of problems that can be resolved by molecular phylogenetics, including the revision of Aporrectodea, Allolobophora, Helodrilus, and Dendrobaena, as well as the examination of small taxa such as Perelia, Eumenescolex, and Iberoscolex. Similar advances have been made with the family Hormogastridae, in which integrative systematics have contributed to the description of several new species, including the delimitation of (formerly) cryptic species. At the family level, integrative systematics have provided a new genus system that better reflects the diversity and biogeography of these earthworms, and phylogenetic comparative methods provide insight into earthworm macroevolution. Despite these achievements, further research should be performed on the Tyrrhenian cryptic complexes, which are of special eco-evolutionary interest. These examples highlight the potential value of applying molecular phylogenetic techniques to other earthworm families, which are very diverse and occupy different terrestrial habitats across the world. The systematic implementation of such approaches should be encouraged among the different expert groups worldwide, with emphasis on collaboration and cooperation.
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38

Marini, Simone, Carla Mavian, Alberto Riva, Mattia Prosperi, Marco Salemi, and Brittany Rife Magalis. "Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics." Bioinformatics 38, no. 3 (October 21, 2021): 856–60. http://dx.doi.org/10.1093/bioinformatics/btab725.

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Abstract Summary TARDiS is a novel phylogenetic tool for optimal genetic subsampling. It optimizes both genetic diversity and temporal distribution through a genetic algorithm. Availability and implementation TARDiS, along with example datasets and a user manual, is available at https://github.com/smarini/tardis-phylogenetics
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39

German, Danielle, Mary Kate Grabowski, and Chris Beyrer. "Enhanced use of phylogenetic data to inform public health approaches to HIV among men who have sex with men." Sexual Health 14, no. 1 (2017): 89. http://dx.doi.org/10.1071/sh16056.

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The multidimensional nature and continued evolution of HIV epidemics among men who have sex with men (MSM) requires innovative intervention approaches. Strategies are needed that recognise the individual, social and structural factors driving HIV transmission; that can pinpoint networks with heightened transmission risk; and that can help target intervention in real time. HIV phylogenetics is a rapidly evolving field with strong promise for informing innovative responses to the HIV epidemic among MSM. Currently, HIV phylogenetic insights are providing new understandings of characteristics of HIV epidemics involving MSM, social networks influencing transmission, characteristics of HIV transmission clusters involving MSM, targets for antiretroviral and other prevention strategies and dynamics of emergent epidemics. Maximising the potential of HIV phylogenetics for HIV responses among MSM will require attention to key methodological challenges and ethical considerations, as well as resolving key implementation and scientific questions. Enhanced and integrated use of HIV surveillance, sociobehavioural and phylogenetic data resources are becoming increasingly critical for informing public health approaches to HIV among MSM.
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40

Ryberg, Martin. "Phylommand - a command line software package for phylogenetics." F1000Research 5 (December 22, 2016): 2903. http://dx.doi.org/10.12688/f1000research.10446.1.

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Phylogenetics is an intrinsic part of many analyses in evolutionary biology and ecology, and as the amount of data available for these analyses is increasing rapidly the need for automated pipelines to deal with the data also increases. Phylommand is a package of four programs to create, manipulate, and/or analyze phylogenetic trees or pairwise alignments. It is built to be easily implemented in software workflows, both directly on the command prompt, and executed using scripts. Inputs can be taken from standard input or a file, and the behavior of the programs can be changed through switches. By using standard file formats for phylogenetic analyses, such as newick, nexus, phylip, and fasta, phylommand is widely compatible with other software.
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41

Zambrano‐Vega, Cristian, Antonio J. Nebro, and José F. Aldana‐Montes. "MO ‐Phylogenetics: a phylogenetic inference software tool with multi‐objective evolutionary metaheuristics." Methods in Ecology and Evolution 7, no. 7 (February 5, 2016): 800–805. http://dx.doi.org/10.1111/2041-210x.12529.

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42

Russo, Claudia A. M., Bárbara Aguiar, Carolina M. Voloch, and Alexandre P. Selvatti. "When Chinese Masks Meet Phylogenetics." American Biology Teacher 78, no. 3 (March 1, 2016): 241–47. http://dx.doi.org/10.1525/abt.2016.78.3.241.

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Phylogenetics has a central role in the biological sciences. We suggest a hands-on exercise to demonstrate the task of character coding and its importance in phylogenetic systematics. This exercise is appropriate for undergraduate students in life sciences and related courses. The teacher must provide a single group of masks in which color patterns, textures, and formats provide the characters to fill the data matrix. (The masks could be replaced by a set of other complex objects.) In this case, because there is no actual phylogeny, students will not be concerned with recovering the correct topology. Character coding is the aim of the exercise. After the character matrix is completed, a phylogenetic tree is drawn and the students interpret the evolution of a single character, starting from the common ancestor, based on the topological pattern of the tree and on the data matrix. In sequence, the students name and provide a full diagnosis for the group of masks as revealed by the topological pattern. The comparison between group results is also educational: there will be some common patterns between trees, but others will differ as in biological systematics.
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43

Wang, Liangliang, Shijia Wang, and Alexandre Bouchard-Côté. "An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics." Systematic Biology 69, no. 1 (June 6, 2019): 155–83. http://dx.doi.org/10.1093/sysbio/syz028.

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Abstract We describe an “embarrassingly parallel” method for Bayesian phylogenetic inference, annealed Sequential Monte Carlo (SMC), based on recent advances in the SMC literature such as adaptive determination of annealing parameters. The algorithm provides an approximate posterior distribution over trees and evolutionary parameters as well as an unbiased estimator for the marginal likelihood. This unbiasedness property can be used for the purpose of testing the correctness of posterior simulation software. We evaluate the performance of phylogenetic annealed SMC by reviewing and comparing with other computational Bayesian phylogenetic methods, in particular, different marginal likelihood estimation methods. Unlike previous SMC methods in phylogenetics, our annealed method can utilize standard Markov chain Monte Carlo (MCMC) tree moves and hence benefit from the large inventory of such moves available in the literature. Consequently, the annealed SMC method should be relatively easy to incorporate into existing phylogenetic software packages based on MCMC algorithms. We illustrate our method using simulation studies and real data analysis.
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44

Sack, Jeffrey D. "Human Evolution and Phylogenetics." American Biology Teacher 67, no. 1 (January 1, 2005): 60. http://dx.doi.org/10.2307/4451781.

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45

ek, M. Micha\l. "Toric varieties in phylogenetics." Dissertationes Mathematicae 511 (2015): 1–86. http://dx.doi.org/10.4064/dm511-0-1.

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46

Ragan, Mark A., Guillaume Bernard, and Cheong Xin Chan. "Molecular phylogenetics before sequences." RNA Biology 11, no. 3 (January 14, 2014): 176–85. http://dx.doi.org/10.4161/rna.27505.

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47

Brown, Stuart M. "Phylogenetics on the Web." BioTechniques 27, no. 6 (December 1999): 1146–48. http://dx.doi.org/10.2144/99276ir01.

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48

Assis, Leandro C. S., and Leandro M. Santos. "Phylogenetics is not phylogenomics." Cladistics 30, no. 1 (May 31, 2013): 8–9. http://dx.doi.org/10.1111/cla.12028.

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49

LANDRY, PIERRE-ALEXANDRE, and FRANCOIS-JOSEPH LAPOINTE. "RAPD problems in phylogenetics." Zoologica Scripta 25, no. 4 (October 1996): 283–90. http://dx.doi.org/10.1111/j.1463-6409.1996.tb00167.x.

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50

Krogmann, Lars, and Hojun Song. "Morphology and integrative phylogenetics." Insect Systematics & Evolution 44, no. 3-4 (2013): 239–40. http://dx.doi.org/10.1163/1876312x-44042106.

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