Computational phylogenetics (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Computational phylogenetics" in English language version.

refsWebsite

Global rank English rank

48nih.gov

4^th place

47doi.org

2^nd place

11semanticscholar.org

11^th place

8^th place

8harvard.edu

18^th place

17^th place

4handle.net

102^nd place

76^th place

4jstor.org

26^th place

20^th place

2books.google.com

3^rd place

1archive.org

6^th place

1kuleuven.be

4,725^th place

3,556^th place

1arxiv.org

69^th place

59^th place

1worldcat.org

5^th place

1archives-ouvertes.fr

1,031^st place

879^th place

1nsf.gov

3,828^th place

2,823^rd place

archive.org

Sokal R, Michener C (1958). "A statistical method for evaluating systematic relationships". University of Kansas Science Bulletin. 38: 1409–1438.

archives-ouvertes.fr

hal.archives-ouvertes.fr

Phillips MJ, Delsuc F, Penny D (July 2004). "Genome-scale phylogeny and the detection of systematic biases" (PDF). Molecular Biology and Evolution. 21 (7): 1455–8. doi:10.1093/molbev/msh137. PMID 15084674.

arxiv.org

Ray S, Jia B, Safavi S, van Opijnen T, Isberg R, Rosch J, Bento J (22 August 2019). "Exact inference under the perfect phylogeny model". arXiv:1908.08623. Bibcode:2019arXiv190808623R. {{cite journal}}: Cite journal requires |journal= (help)

books.google.com

Mount DM (2004). Bioinformatics: Sequence and Genome Analysis (2nd ed.). Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. ISBN 978-0-87969-712-9.
Baum DA, Smith SD (2013). Tree Thinking: An Introduction to Phylogenetic Biology. Roberts. p. 442. ISBN 978-1-936221-16-5.

doi.org

Gaubert P, Wozencraft WC, Cordeiro-Estrela P, Veron G (December 2005). "Mosaics of convergences and noise in morphological phylogenies: what's in a viverrid-like carnivoran?". Systematic Biology. 54 (6): 865–94. doi:10.1080/10635150500232769. PMID 16282167.
Strait DS, Grine FE (December 2004). "Inferring hominoid and early hominid phylogeny using craniodental characters: the role of fossil taxa". Journal of Human Evolution. 47 (6): 399–452. Bibcode:2004JHumE..47..399S. doi:10.1016/j.jhevol.2004.08.008. PMID 15566946.
Wiens JJ (2001). "Character analysis in morphological phylogenetics: problems and solutions". Systematic Biology. 50 (5): 689–99. doi:10.1080/106351501753328811. PMID 12116939.
Jenner RA (2001). "Bilaterian phylogeny and uncritical recycling of morphological data sets". Systematic Biology. 50 (5): 730–42. doi:10.1080/106351501753328857. PMID 12116943.
Saitou N, Nei M (July 1987). "The neighbor-joining method: a new method for reconstructing phylogenetic trees". Molecular Biology and Evolution. 4 (4): 406–25. doi:10.1093/oxfordjournals.molbev.a040454. PMID 3447015.
Fitch WM, Margoliash E (January 1967). "Construction of phylogenetic trees". Science. 155 (3760): 279–84. Bibcode:1967Sci...155..279F. doi:10.1126/science.155.3760.279. PMID 5334057.
Lespinats S, Grando D, Maréchal E, Hakimi MA, Tenaillon O, Bastien O (2011). "How Fitch-Margoliash Algorithm can Benefit from Multi Dimensional Scaling". Evolutionary Bioinformatics Online. 7: 61–85. doi:10.4137/EBO.S7048. PMC 3118699. PMID 21697992.
Day WH (1987). "Computational complexity of inferring phylogenies from dissimilarity matrices". Bulletin of Mathematical Biology. 49 (4): 461–7. doi:10.1007/BF02458863. PMID 3664032. S2CID 189885258.
Hendy MD, Penny D (1982). "Branch and bound algorithms to determine minimal evolutionary trees". Mathematical Biosciences. 59 (2): 277–290. doi:10.1016/0025-5564(82)90027-X.
Sankoff D, Morel C, Cedergren RJ (October 1973). "Evolution of 5S RNA and the non-randomness of base replacement". Nature. 245 (147): 232–4. doi:10.1038/newbio245232a0. PMID 4201431.
Wheeler WC, Gladstein DS (1994). "MALIGN: a multiple nucleic acid sequence alignment program". Journal of Heredity. 85 (5): 417–418. doi:10.1093/oxfordjournals.jhered.a111492.
Simmons MP (June 2004). "Independence of alignment and tree search". Molecular Phylogenetics and Evolution. 31 (3): 874–9. Bibcode:2004MolPE..31..874S. doi:10.1016/j.ympev.2003.10.008. PMID 15120385.
De Laet J (2015). "Parsimony analysis of unaligned sequence data: maximization of homology and minimization of homoplasy, not Minimization of operationally defined total cost or minimization of equally weighted transformations". Cladistics. 31 (5): 550–567. doi:10.1111/cla.12098. PMID 34772278. S2CID 221582410.
Chor B, Tuller T (June 2005). "Maximum likelihood of evolutionary trees: hardness and approximation". Bioinformatics. 21 (Suppl 1): i97–106. doi:10.1093/bioinformatics/bti1027. PMID 15961504.
El-Kebir M, Oesper L, Acheson-Field H, Raphael BJ (June 2015). "Reconstruction of clonal trees and tumor composition from multi-sample sequencing data". Bioinformatics. 31 (12): i62-70. doi:10.1093/bioinformatics/btv261. PMC 4542783. PMID 26072510.
Malikic S, McPherson AW, Donmez N, Sahinalp CS (May 2015). "Clonality inference in multiple tumor samples using phylogeny". Bioinformatics. 31 (9): 1349–56. doi:10.1093/bioinformatics/btv003. PMID 25568283.
Mau B, Newton MA (1997). "Phylogenetic inference for binary data on dendrograms using Markov chain Monte Carlo". Journal of Computational and Graphical Statistics. 6 (1): 122–131. doi:10.2307/1390728. JSTOR 1390728.
Yang Z, Rannala B (July 1997). "Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method". Molecular Biology and Evolution. 14 (7): 717–24. doi:10.1093/oxfordjournals.molbev.a025811. PMID 9214744.
Kolaczkowski B, Thornton JW (December 2009). Delport W (ed.). "Long-branch attraction bias and inconsistency in Bayesian phylogenetics". PLOS ONE. 4 (12): e7891. Bibcode:2009PLoSO...4.7891K. doi:10.1371/journal.pone.0007891. PMC 2785476. PMID 20011052.
Simmons MP (2012). "Misleading results of likelihood-based phylogenetic analyses in the presence of missing data". Cladistics. 28 (2): 208–222. doi:10.1111/j.1096-0031.2011.00375.x. PMID 34872185. S2CID 53123024.
Larget B (July 2013). "The estimation of tree posterior probabilities using conditional clade probability distributions". Systematic Biology. 62 (4): 501–11. doi:10.1093/sysbio/syt014. PMC 3676676. PMID 23479066.
Jiang Y, Qiu Y, Minn AJ, Zhang NR (September 2016). "Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing". Proceedings of the National Academy of Sciences of the United States of America. 113 (37): E5528-37. Bibcode:2016PNAS..113E5528J. doi:10.1073/pnas.1522203113. PMC 5027458. PMID 27573852.
Deshwar AG, Vembu S, Yung CK, Jang GH, Stein L, Morris Q (February 2015). "PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors". Genome Biology. 16 (1): 35. doi:10.1186/s13059-015-0602-8. PMC 4359439. PMID 25786235.
Sullivan J, Joyce P (2005). "Model Selection in Phylogenetics". Annual Review of Ecology, Evolution, and Systematics. 36 (1): 445–466. doi:10.1146/annurev.ecolsys.36.102003.152633. PMC 3144157. PMID 20671039.
Galtier N, Gouy M (July 1998). "Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis". Molecular Biology and Evolution. 15 (7): 871–9. doi:10.1093/oxfordjournals.molbev.a025991. PMID 9656487.
Fitch WM, Markowitz E (October 1970). "An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution". Biochemical Genetics. 4 (5): 579–93. doi:10.1007/bf00486096. PMID 5489762. S2CID 26638948.
Pol D (December 2004). "Empirical problems of the hierarchical likelihood ratio test for model selection". Systematic Biology. 53 (6): 949–62. doi:10.1080/10635150490888868. PMID 15764562.
Abadi S, Azouri D, Pupko T, Mayrose I (February 2019). "Model selection may not be a mandatory step for phylogeny reconstruction". Nature Communications. 10 (1): 934. Bibcode:2019NatCo..10..934A. doi:10.1038/s41467-019-08822-w. PMC 6389923. PMID 30804347.
Bast F (2013). "Sequence similarity search, Multiple Sequence Alignment, Model Selection, Distance Matrix and Phylogeny Reconstruction". Protocol Exchange. doi:10.1038/protex.2013.065.
Ruan Y, House GL, Ekanayake S, Schütte U, Bever JD, Tang H, Fox G (26 May 2014). "Integration of clustering and multidimensional scaling to determine phylogenetic trees as spherical phylograms visualized in 3 dimensions". 2014 14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing. IEEE. pp. 720–729. doi:10.1109/CCGrid.2014.126. ISBN 978-1-4799-2784-5. S2CID 9581901.
Felsenstein J (July 1985). "Confidence Limits on Phylogenies: An Approach Using the Bootstrap". Evolution; International Journal of Organic Evolution. 39 (4): 783–791. doi:10.2307/2408678. JSTOR 2408678. PMID 28561359.
Hillis DM, Bull JJ (1993). "An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis". Systematic Biology. 42 (2): 182–192. doi:10.1093/sysbio/42.2.182. ISSN 1063-5157.
Huelsenbeck J, Rannala B (December 2004). "Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models". Systematic Biology. 53 (6): 904–13. doi:10.1080/10635150490522629. PMID 15764559.
Chemisquy MA, Prevosti FJ (2013). "Evaluating the clade size effect in alternative measures of branch support". Journal of Zoological Systematics and Evolutionary Research. 51 (4): 260–273. doi:10.1111/jzs.12024. hdl:11336/4144.
Phillips MJ, Delsuc F, Penny D (July 2004). "Genome-scale phylogeny and the detection of systematic biases" (PDF). Molecular Biology and Evolution. 21 (7): 1455–8. doi:10.1093/molbev/msh137. PMID 15084674.
Goloboff PA, Carpenter JM, Arias JS, Esquivel DR (2008). "Weighting against homoplasy improves phylogenetic analysis of morphological data sets". Cladistics. 24 (5): 758–773. doi:10.1111/j.1096-0031.2008.00209.x. hdl:11336/82003. S2CID 913161.
Goloboff PA (1997). "Self-Weighted Optimization: Tree Searches and Character State Reconstructions under Implied Transformation Costs". Cladistics. 13 (3): 225–245. doi:10.1111/j.1096-0031.1997.tb00317.x. PMID 34911233. S2CID 196595734.
Funk DJ, Omland KE (2003). "Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA". Annual Review of Ecology, Evolution, and Systematics. 34: 397–423. doi:10.1146/annurev.ecolsys.34.011802.132421. S2CID 33951905.
Kutschera VE, Bidon T, Hailer F, Rodi J, Fain SR, Janke A (2014). "Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow". Molecular Biology and Evolution. 31 (8): 2004–2017. doi:10.1093/molbev/msu186. PMC 4104321. PMID 24903145.
Qu Y, Zhang R, Quan Q, Song G, Li SH, Lei F (December 2012). "Incomplete lineage sorting or secondary admixture: disentangling historical divergence from recent gene flow in the Vinous-throated parrotbill (Paradoxornis webbianus)". Molecular Ecology. 21 (24): 6117–33. Bibcode:2012MolEc..21.6117Q. doi:10.1111/mec.12080. PMID 23095021. S2CID 22635918.
Pollard DA, Iyer VN, Moses AM, Eisen MB (October 2006). "Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting". PLOS Genetics. 2 (10): e173. doi:10.1371/journal.pgen.0020173. PMC 1626107. PMID 17132051.
Zwickl DJ, Hillis DM (August 2002). "Increased taxon sampling greatly reduces phylogenetic error". Systematic Biology. 51 (4): 588–98. doi:10.1080/10635150290102339. PMID 12228001.
Wiens JJ (February 2006). "Missing data and the design of phylogenetic analyses". Journal of Biomedical Informatics. 39 (1): 34–42. doi:10.1016/j.jbi.2005.04.001. PMID 15922672.
Blomberg SP, Garland T, Ives AR (April 2003). "Testing for phylogenetic signal in comparative data: behavioral traits are more labile". Evolution; International Journal of Organic Evolution. 57 (4): 717–45. doi:10.1111/j.0014-3820.2003.tb00285.x. PMID 12778543. S2CID 221735844.
Archie JW (1985). "Methods for coding variable morphological features for numerical taxonomic analysis". Systematic Zoology. 34 (3): 326–345. doi:10.2307/2413151. JSTOR 2413151.
Prevosti FJ, Chemisquy MA (2009). "The impact of missing data on real morphological phylogenies: Influence of the number and distribution of missing entries". Cladistics. 26 (3): 326–339. doi:10.1111/j.1096-0031.2009.00289.x. hdl:11336/69010. PMID 34875786. S2CID 86850694.
Cobbett A, Wilkinson M, Wills MA (October 2007). "Fossils impact as hard as living taxa in parsimony analyses of morphology". Systematic Biology. 56 (5): 753–66. doi:10.1080/10635150701627296. PMID 17886145.

handle.net

hdl.handle.net

Khalafvand, Tyler (2015). Finding Structure in the Phylogeny Search Space (MCSc thesis). Dalhousie University.
Chemisquy MA, Prevosti FJ (2013). "Evaluating the clade size effect in alternative measures of branch support". Journal of Zoological Systematics and Evolutionary Research. 51 (4): 260–273. doi:10.1111/jzs.12024. hdl:11336/4144.
Goloboff PA, Carpenter JM, Arias JS, Esquivel DR (2008). "Weighting against homoplasy improves phylogenetic analysis of morphological data sets". Cladistics. 24 (5): 758–773. doi:10.1111/j.1096-0031.2008.00209.x. hdl:11336/82003. S2CID 913161.
Prevosti FJ, Chemisquy MA (2009). "The impact of missing data on real morphological phylogenies: Influence of the number and distribution of missing entries". Cladistics. 26 (3): 326–339. doi:10.1111/j.1096-0031.2009.00289.x. hdl:11336/69010. PMID 34875786. S2CID 86850694.

harvard.edu

ui.adsabs.harvard.edu

Strait DS, Grine FE (December 2004). "Inferring hominoid and early hominid phylogeny using craniodental characters: the role of fossil taxa". Journal of Human Evolution. 47 (6): 399–452. Bibcode:2004JHumE..47..399S. doi:10.1016/j.jhevol.2004.08.008. PMID 15566946.
Fitch WM, Margoliash E (January 1967). "Construction of phylogenetic trees". Science. 155 (3760): 279–84. Bibcode:1967Sci...155..279F. doi:10.1126/science.155.3760.279. PMID 5334057.
Simmons MP (June 2004). "Independence of alignment and tree search". Molecular Phylogenetics and Evolution. 31 (3): 874–9. Bibcode:2004MolPE..31..874S. doi:10.1016/j.ympev.2003.10.008. PMID 15120385.
Kolaczkowski B, Thornton JW (December 2009). Delport W (ed.). "Long-branch attraction bias and inconsistency in Bayesian phylogenetics". PLOS ONE. 4 (12): e7891. Bibcode:2009PLoSO...4.7891K. doi:10.1371/journal.pone.0007891. PMC 2785476. PMID 20011052.
Ray S, Jia B, Safavi S, van Opijnen T, Isberg R, Rosch J, Bento J (22 August 2019). "Exact inference under the perfect phylogeny model". arXiv:1908.08623. Bibcode:2019arXiv190808623R. {{cite journal}}: Cite journal requires |journal= (help)
Jiang Y, Qiu Y, Minn AJ, Zhang NR (September 2016). "Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing". Proceedings of the National Academy of Sciences of the United States of America. 113 (37): E5528-37. Bibcode:2016PNAS..113E5528J. doi:10.1073/pnas.1522203113. PMC 5027458. PMID 27573852.
Abadi S, Azouri D, Pupko T, Mayrose I (February 2019). "Model selection may not be a mandatory step for phylogeny reconstruction". Nature Communications. 10 (1): 934. Bibcode:2019NatCo..10..934A. doi:10.1038/s41467-019-08822-w. PMC 6389923. PMID 30804347.
Qu Y, Zhang R, Quan Q, Song G, Li SH, Lei F (December 2012). "Incomplete lineage sorting or secondary admixture: disentangling historical divergence from recent gene flow in the Vinous-throated parrotbill (Paradoxornis webbianus)". Molecular Ecology. 21 (24): 6117–33. Bibcode:2012MolEc..21.6117Q. doi:10.1111/mec.12080. PMID 23095021. S2CID 22635918.

jstor.org

Swiderski DL, Zelditch ML, Fink WL (September 1998). "Why morphometrics is not special: coding quantitative data for phylogenetic analysis". Systematic Biology. 47 (3): 508–19. JSTOR 2585256. PMID 12066691.
Mau B, Newton MA (1997). "Phylogenetic inference for binary data on dendrograms using Markov chain Monte Carlo". Journal of Computational and Graphical Statistics. 6 (1): 122–131. doi:10.2307/1390728. JSTOR 1390728.
Felsenstein J (July 1985). "Confidence Limits on Phylogenies: An Approach Using the Bootstrap". Evolution; International Journal of Organic Evolution. 39 (4): 783–791. doi:10.2307/2408678. JSTOR 2408678. PMID 28561359.
Archie JW (1985). "Methods for coding variable morphological features for numerical taxonomic analysis". Systematic Zoology. 34 (3): 326–345. doi:10.2307/2413151. JSTOR 2413151.

kuleuven.be

lirias.kuleuven.be

De Laet J (2015). "Parsimony analysis of unaligned sequence data: maximization of homology and minimization of homoplasy, not Minimization of operationally defined total cost or minimization of equally weighted transformations". Cladistics. 31 (5): 550–567. doi:10.1111/cla.12098. PMID 34772278. S2CID 221582410.

nih.gov

pubmed.ncbi.nlm.nih.gov

Swiderski DL, Zelditch ML, Fink WL (September 1998). "Why morphometrics is not special: coding quantitative data for phylogenetic analysis". Systematic Biology. 47 (3): 508–19. JSTOR 2585256. PMID 12066691.
Gaubert P, Wozencraft WC, Cordeiro-Estrela P, Veron G (December 2005). "Mosaics of convergences and noise in morphological phylogenies: what's in a viverrid-like carnivoran?". Systematic Biology. 54 (6): 865–94. doi:10.1080/10635150500232769. PMID 16282167.
Strait DS, Grine FE (December 2004). "Inferring hominoid and early hominid phylogeny using craniodental characters: the role of fossil taxa". Journal of Human Evolution. 47 (6): 399–452. Bibcode:2004JHumE..47..399S. doi:10.1016/j.jhevol.2004.08.008. PMID 15566946.
Wiens JJ (2001). "Character analysis in morphological phylogenetics: problems and solutions". Systematic Biology. 50 (5): 689–99. doi:10.1080/106351501753328811. PMID 12116939.
Jenner RA (2001). "Bilaterian phylogeny and uncritical recycling of morphological data sets". Systematic Biology. 50 (5): 730–42. doi:10.1080/106351501753328857. PMID 12116943.
Saitou N, Nei M (July 1987). "The neighbor-joining method: a new method for reconstructing phylogenetic trees". Molecular Biology and Evolution. 4 (4): 406–25. doi:10.1093/oxfordjournals.molbev.a040454. PMID 3447015.
Fitch WM, Margoliash E (January 1967). "Construction of phylogenetic trees". Science. 155 (3760): 279–84. Bibcode:1967Sci...155..279F. doi:10.1126/science.155.3760.279. PMID 5334057.
Lespinats S, Grando D, Maréchal E, Hakimi MA, Tenaillon O, Bastien O (2011). "How Fitch-Margoliash Algorithm can Benefit from Multi Dimensional Scaling". Evolutionary Bioinformatics Online. 7: 61–85. doi:10.4137/EBO.S7048. PMC 3118699. PMID 21697992.
Day WH (1987). "Computational complexity of inferring phylogenies from dissimilarity matrices". Bulletin of Mathematical Biology. 49 (4): 461–7. doi:10.1007/BF02458863. PMID 3664032. S2CID 189885258.
Sankoff D, Morel C, Cedergren RJ (October 1973). "Evolution of 5S RNA and the non-randomness of base replacement". Nature. 245 (147): 232–4. doi:10.1038/newbio245232a0. PMID 4201431.
Simmons MP (June 2004). "Independence of alignment and tree search". Molecular Phylogenetics and Evolution. 31 (3): 874–9. Bibcode:2004MolPE..31..874S. doi:10.1016/j.ympev.2003.10.008. PMID 15120385.
De Laet J (2015). "Parsimony analysis of unaligned sequence data: maximization of homology and minimization of homoplasy, not Minimization of operationally defined total cost or minimization of equally weighted transformations". Cladistics. 31 (5): 550–567. doi:10.1111/cla.12098. PMID 34772278. S2CID 221582410.
Chor B, Tuller T (June 2005). "Maximum likelihood of evolutionary trees: hardness and approximation". Bioinformatics. 21 (Suppl 1): i97–106. doi:10.1093/bioinformatics/bti1027. PMID 15961504.
El-Kebir M, Oesper L, Acheson-Field H, Raphael BJ (June 2015). "Reconstruction of clonal trees and tumor composition from multi-sample sequencing data". Bioinformatics. 31 (12): i62-70. doi:10.1093/bioinformatics/btv261. PMC 4542783. PMID 26072510.
Malikic S, McPherson AW, Donmez N, Sahinalp CS (May 2015). "Clonality inference in multiple tumor samples using phylogeny". Bioinformatics. 31 (9): 1349–56. doi:10.1093/bioinformatics/btv003. PMID 25568283.
Yang Z, Rannala B (July 1997). "Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method". Molecular Biology and Evolution. 14 (7): 717–24. doi:10.1093/oxfordjournals.molbev.a025811. PMID 9214744.
Kolaczkowski B, Thornton JW (December 2009). Delport W (ed.). "Long-branch attraction bias and inconsistency in Bayesian phylogenetics". PLOS ONE. 4 (12): e7891. Bibcode:2009PLoSO...4.7891K. doi:10.1371/journal.pone.0007891. PMC 2785476. PMID 20011052.
Simmons MP (2012). "Misleading results of likelihood-based phylogenetic analyses in the presence of missing data". Cladistics. 28 (2): 208–222. doi:10.1111/j.1096-0031.2011.00375.x. PMID 34872185. S2CID 53123024.
Larget B (July 2013). "The estimation of tree posterior probabilities using conditional clade probability distributions". Systematic Biology. 62 (4): 501–11. doi:10.1093/sysbio/syt014. PMC 3676676. PMID 23479066.
Jiang Y, Qiu Y, Minn AJ, Zhang NR (September 2016). "Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing". Proceedings of the National Academy of Sciences of the United States of America. 113 (37): E5528-37. Bibcode:2016PNAS..113E5528J. doi:10.1073/pnas.1522203113. PMC 5027458. PMID 27573852.
Deshwar AG, Vembu S, Yung CK, Jang GH, Stein L, Morris Q (February 2015). "PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors". Genome Biology. 16 (1): 35. doi:10.1186/s13059-015-0602-8. PMC 4359439. PMID 25786235.
Sullivan J, Joyce P (2005). "Model Selection in Phylogenetics". Annual Review of Ecology, Evolution, and Systematics. 36 (1): 445–466. doi:10.1146/annurev.ecolsys.36.102003.152633. PMC 3144157. PMID 20671039.
Galtier N, Gouy M (July 1998). "Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis". Molecular Biology and Evolution. 15 (7): 871–9. doi:10.1093/oxfordjournals.molbev.a025991. PMID 9656487.
Fitch WM, Markowitz E (October 1970). "An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution". Biochemical Genetics. 4 (5): 579–93. doi:10.1007/bf00486096. PMID 5489762. S2CID 26638948.
Pol D (December 2004). "Empirical problems of the hierarchical likelihood ratio test for model selection". Systematic Biology. 53 (6): 949–62. doi:10.1080/10635150490888868. PMID 15764562.
Abadi S, Azouri D, Pupko T, Mayrose I (February 2019). "Model selection may not be a mandatory step for phylogeny reconstruction". Nature Communications. 10 (1): 934. Bibcode:2019NatCo..10..934A. doi:10.1038/s41467-019-08822-w. PMC 6389923. PMID 30804347.
Felsenstein J (July 1985). "Confidence Limits on Phylogenies: An Approach Using the Bootstrap". Evolution; International Journal of Organic Evolution. 39 (4): 783–791. doi:10.2307/2408678. JSTOR 2408678. PMID 28561359.
Huelsenbeck J, Rannala B (December 2004). "Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models". Systematic Biology. 53 (6): 904–13. doi:10.1080/10635150490522629. PMID 15764559.
Phillips MJ, Delsuc F, Penny D (July 2004). "Genome-scale phylogeny and the detection of systematic biases" (PDF). Molecular Biology and Evolution. 21 (7): 1455–8. doi:10.1093/molbev/msh137. PMID 15084674.
Goloboff PA (1997). "Self-Weighted Optimization: Tree Searches and Character State Reconstructions under Implied Transformation Costs". Cladistics. 13 (3): 225–245. doi:10.1111/j.1096-0031.1997.tb00317.x. PMID 34911233. S2CID 196595734.
Kutschera VE, Bidon T, Hailer F, Rodi J, Fain SR, Janke A (2014). "Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow". Molecular Biology and Evolution. 31 (8): 2004–2017. doi:10.1093/molbev/msu186. PMC 4104321. PMID 24903145.
Qu Y, Zhang R, Quan Q, Song G, Li SH, Lei F (December 2012). "Incomplete lineage sorting or secondary admixture: disentangling historical divergence from recent gene flow in the Vinous-throated parrotbill (Paradoxornis webbianus)". Molecular Ecology. 21 (24): 6117–33. Bibcode:2012MolEc..21.6117Q. doi:10.1111/mec.12080. PMID 23095021. S2CID 22635918.
Pollard DA, Iyer VN, Moses AM, Eisen MB (October 2006). "Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting". PLOS Genetics. 2 (10): e173. doi:10.1371/journal.pgen.0020173. PMC 1626107. PMID 17132051.
Zwickl DJ, Hillis DM (August 2002). "Increased taxon sampling greatly reduces phylogenetic error". Systematic Biology. 51 (4): 588–98. doi:10.1080/10635150290102339. PMID 12228001.
Wiens JJ (February 2006). "Missing data and the design of phylogenetic analyses". Journal of Biomedical Informatics. 39 (1): 34–42. doi:10.1016/j.jbi.2005.04.001. PMID 15922672.
Blomberg SP, Garland T, Ives AR (April 2003). "Testing for phylogenetic signal in comparative data: behavioral traits are more labile". Evolution; International Journal of Organic Evolution. 57 (4): 717–45. doi:10.1111/j.0014-3820.2003.tb00285.x. PMID 12778543. S2CID 221735844.
Prevosti FJ, Chemisquy MA (2009). "The impact of missing data on real morphological phylogenies: Influence of the number and distribution of missing entries". Cladistics. 26 (3): 326–339. doi:10.1111/j.1096-0031.2009.00289.x. hdl:11336/69010. PMID 34875786. S2CID 86850694.
Cobbett A, Wilkinson M, Wills MA (October 2007). "Fossils impact as hard as living taxa in parsimony analyses of morphology". Systematic Biology. 56 (5): 753–66. doi:10.1080/10635150701627296. PMID 17886145.

ncbi.nlm.nih.gov

Lespinats S, Grando D, Maréchal E, Hakimi MA, Tenaillon O, Bastien O (2011). "How Fitch-Margoliash Algorithm can Benefit from Multi Dimensional Scaling". Evolutionary Bioinformatics Online. 7: 61–85. doi:10.4137/EBO.S7048. PMC 3118699. PMID 21697992.
El-Kebir M, Oesper L, Acheson-Field H, Raphael BJ (June 2015). "Reconstruction of clonal trees and tumor composition from multi-sample sequencing data". Bioinformatics. 31 (12): i62-70. doi:10.1093/bioinformatics/btv261. PMC 4542783. PMID 26072510.
Kolaczkowski B, Thornton JW (December 2009). Delport W (ed.). "Long-branch attraction bias and inconsistency in Bayesian phylogenetics". PLOS ONE. 4 (12): e7891. Bibcode:2009PLoSO...4.7891K. doi:10.1371/journal.pone.0007891. PMC 2785476. PMID 20011052.
Larget B (July 2013). "The estimation of tree posterior probabilities using conditional clade probability distributions". Systematic Biology. 62 (4): 501–11. doi:10.1093/sysbio/syt014. PMC 3676676. PMID 23479066.
Jiang Y, Qiu Y, Minn AJ, Zhang NR (September 2016). "Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing". Proceedings of the National Academy of Sciences of the United States of America. 113 (37): E5528-37. Bibcode:2016PNAS..113E5528J. doi:10.1073/pnas.1522203113. PMC 5027458. PMID 27573852.
Deshwar AG, Vembu S, Yung CK, Jang GH, Stein L, Morris Q (February 2015). "PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors". Genome Biology. 16 (1): 35. doi:10.1186/s13059-015-0602-8. PMC 4359439. PMID 25786235.
Sullivan J, Joyce P (2005). "Model Selection in Phylogenetics". Annual Review of Ecology, Evolution, and Systematics. 36 (1): 445–466. doi:10.1146/annurev.ecolsys.36.102003.152633. PMC 3144157. PMID 20671039.
Abadi S, Azouri D, Pupko T, Mayrose I (February 2019). "Model selection may not be a mandatory step for phylogeny reconstruction". Nature Communications. 10 (1): 934. Bibcode:2019NatCo..10..934A. doi:10.1038/s41467-019-08822-w. PMC 6389923. PMID 30804347.
Kutschera VE, Bidon T, Hailer F, Rodi J, Fain SR, Janke A (2014). "Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow". Molecular Biology and Evolution. 31 (8): 2004–2017. doi:10.1093/molbev/msu186. PMC 4104321. PMID 24903145.
Pollard DA, Iyer VN, Moses AM, Eisen MB (October 2006). "Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting". PLOS Genetics. 2 (10): e173. doi:10.1371/journal.pgen.0020173. PMC 1626107. PMID 17132051.

nsf.gov

"Genealogy of Life (GoLife)". National Science Foundation. Retrieved 5 May 2015. The GoLife program builds upon the AToL program by accommodating the complexity of diversification patterns across all of life's history. Our current knowledge of processes such as hybridization, endosymbiosis and lateral gene transfer makes clear that the evolutionary history of life on Earth cannot accurately be depicted - for every branch of the tree - as a single, typological, bifurcating tree.

semanticscholar.org

api.semanticscholar.org

Day WH (1987). "Computational complexity of inferring phylogenies from dissimilarity matrices". Bulletin of Mathematical Biology. 49 (4): 461–7. doi:10.1007/BF02458863. PMID 3664032. S2CID 189885258.
De Laet J (2015). "Parsimony analysis of unaligned sequence data: maximization of homology and minimization of homoplasy, not Minimization of operationally defined total cost or minimization of equally weighted transformations". Cladistics. 31 (5): 550–567. doi:10.1111/cla.12098. PMID 34772278. S2CID 221582410.
Simmons MP (2012). "Misleading results of likelihood-based phylogenetic analyses in the presence of missing data". Cladistics. 28 (2): 208–222. doi:10.1111/j.1096-0031.2011.00375.x. PMID 34872185. S2CID 53123024.
Fitch WM, Markowitz E (October 1970). "An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution". Biochemical Genetics. 4 (5): 579–93. doi:10.1007/bf00486096. PMID 5489762. S2CID 26638948.
Ruan Y, House GL, Ekanayake S, Schütte U, Bever JD, Tang H, Fox G (26 May 2014). "Integration of clustering and multidimensional scaling to determine phylogenetic trees as spherical phylograms visualized in 3 dimensions". 2014 14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing. IEEE. pp. 720–729. doi:10.1109/CCGrid.2014.126. ISBN 978-1-4799-2784-5. S2CID 9581901.
Goloboff PA, Carpenter JM, Arias JS, Esquivel DR (2008). "Weighting against homoplasy improves phylogenetic analysis of morphological data sets". Cladistics. 24 (5): 758–773. doi:10.1111/j.1096-0031.2008.00209.x. hdl:11336/82003. S2CID 913161.
Goloboff PA (1997). "Self-Weighted Optimization: Tree Searches and Character State Reconstructions under Implied Transformation Costs". Cladistics. 13 (3): 225–245. doi:10.1111/j.1096-0031.1997.tb00317.x. PMID 34911233. S2CID 196595734.
Funk DJ, Omland KE (2003). "Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA". Annual Review of Ecology, Evolution, and Systematics. 34: 397–423. doi:10.1146/annurev.ecolsys.34.011802.132421. S2CID 33951905.
Qu Y, Zhang R, Quan Q, Song G, Li SH, Lei F (December 2012). "Incomplete lineage sorting or secondary admixture: disentangling historical divergence from recent gene flow in the Vinous-throated parrotbill (Paradoxornis webbianus)". Molecular Ecology. 21 (24): 6117–33. Bibcode:2012MolEc..21.6117Q. doi:10.1111/mec.12080. PMID 23095021. S2CID 22635918.
Blomberg SP, Garland T, Ives AR (April 2003). "Testing for phylogenetic signal in comparative data: behavioral traits are more labile". Evolution; International Journal of Organic Evolution. 57 (4): 717–45. doi:10.1111/j.0014-3820.2003.tb00285.x. PMID 12778543. S2CID 221735844.
Prevosti FJ, Chemisquy MA (2009). "The impact of missing data on real morphological phylogenies: Influence of the number and distribution of missing entries". Cladistics. 26 (3): 326–339. doi:10.1111/j.1096-0031.2009.00289.x. hdl:11336/69010. PMID 34875786. S2CID 86850694.

worldcat.org

search.worldcat.org

Hillis DM, Bull JJ (1993). "An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis". Systematic Biology. 42 (2): 182–192. doi:10.1093/sysbio/42.2.182. ISSN 1063-5157.