Publications related to 'from sequences'
 
Order by:   Type | Year
           related to:
Associated keywords
Article (Journal)
1
photophotophoto
Hans-Jürgen Bandelt, Peter Forster and Arne Röhl. Median-joining networks for inferring intraspecies phylogenies. In MBE, Vol. 16(1):37-48, 1999.
Keywords: from sequences, median network, MedianJoining, Program Network, reconstruction, software.
Note: http://mbe.oxfordjournals.org/cgi/content/abstract/16/1/37.
       

2
photophotophoto
Hans-Jürgen Bandelt, Vincent Macaulay and Martin Richards. Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA. In MPE, Vol. 16:8-28, 2000.
Keywords: from sequences, from splits, median network, phylogenetic network, phylogeny, reconstruction.
Note: http://www.stats.gla.ac.uk/~vincent/papers/speedy.pdf.
       
Toggle abstract
3
photophotophoto
Mark Clement, David Posada and Keith A. Crandall. TCS: a computer program to estimate gene genealogies. In MOLE, Vol. 9:1657-1659, 2000.
Keywords: from sequences, parsimony, phylogenetic network, phylogeny, Program TCS, reconstruction, software, statistical parsimony.
Note: http://darwin.uvigo.es/download/papers/08.tcs00.pdf.
       
Toggle abstract
4
photophotophoto
Dan Gusfield, Satish Eddhu and Charles Langley. Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. In JBCB, Vol. 2(1):173-213, 2004.
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, recombination, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/exfinalrec.pdf.
       
Toggle abstract
5
photophotophoto
Dan Gusfield, Satish Eddhu and Charles Langley. The fine structure of galls in phylogenetic networks. In INCOMP, Vol. 16(4):459-469, 2004.
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/informs.pdf.
       
Toggle abstract
6
photo
Jotun Hein. A heuristic method to reconstruct the history of sequences subject to recombination. In JME, Vol. 36(4):396-405, 1993.
Keywords: explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny, Program RecPars, recombination, recombination detection, software.
Note: http://dx.doi.org/10.1007/BF00182187.
       

7
photophoto
John Kececioglu and Dan Gusfield. Reconstructing a history of recombinations from a set of sequences. In DAM, Pages 239-260, 1998.
Keywords: from sequences, NP complete, polynomial, recombination, reconstruction.
Note: http://citeseer.ist.psu.edu/76600.html.
       

8
photophotophotophoto
Cam Thach Nguyen, Nguyen Bao Nguyen, Wing-Kin Sung and Louxin Zhang. Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem. In TCBB, Vol. 4(3):394-402, 2007.
Keywords: explicit network, from sequences, labeling, NP complete, parsimony, phylogenetic network, phylogeny.
Note: http://www.cs.washington.edu/homes/ncthach/Papers/TCBB2007.pdf.
       

9
photophotophoto
Alan R. Templeton, Keith A. Crandall and Charles F. Sing. A Cladistic Analysis of Phenotypic Associations With Haplotypes Inferred From Restriction Endonuclease Mapping and DNA Sequence Data. III. Cladogram Estimation. In GEN, Vol. 132:619-633, 2000.
Keywords: from sequences, parsimony, phylogenetic network, phylogeny, Program TCS, recombination, reconstruction, statistical parsimony.
Note: http://www.genetics.org/cgi/content/abstract/132/2/619.
       

10
photophotophotophoto
Dan Gusfield, Vikas Bansal, Vineet Bafna and Yun S. Song. A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. In JCB, Vol. 14(10):1247-1272, 2007.
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, Program Beagle, Program GalledTree, recombination, reconstruction, software.
Note: http://www.eecs.berkeley.edu/~yss/Pub/decomposition.pdf.
       

11
photophoto
Kirill Kryukov and Naruya Saitou. Netview: Application Software for Constructing and Visually Exploring Phylogenetic Networks. In Genome Informatics, Vol. 14:280-281, 2003.
Keywords: from sequences, phylogenetic network, phylogeny, Program NetView, visualization.
Note: http://www.jsbi.org/journal/GIW03/GIW03SS06.pdf.
       

12
photophotophotophotophoto
Yun S. Song, Zhihong Ding, Dan Gusfield, Charles Langley and Yufeng Wu. Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. In JCB, Vol. 14(10):1273-1286, 2007.
Keywords: ARG, from sequences, phylogenetic network, phylogeny, Program SHRUB, reconstruction.
Note: http://dx.doi.org/10.1089/cmb.2007.0096.
       
Toggle abstract
13
photo
Yun S. Song. A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree. In TCBB, Vol. 3(2):186-191, 2006.
Keywords: characterization, from sequences, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.eecs.berkeley.edu/~yss/Pub/nasc4gall.pdf.
       

14
photophoto
Patricia Buendia and Giri Narasimhan. Sliding MinPD: Building evolutionary networks of serial samples via an automated recombination detection approach. In BIO, Vol. 23(22):2993-3000, 2007.
Keywords: from sequences, phylogenetic network, phylogeny, Program Sliding MinPD, recombination, recombination detection, serial evolutionary networks, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btm413.
       
Toggle abstract
15
photophoto
Supriya Munshaw and Thomas B. Kepler. An Information-Theoretic Method for the Treatment of Plural Ancestry in Phylogenetics. In MBE, Vol. 25(6):1199-1208, 2008.
Keywords: explicit network, from sequences, heuristic, phylogenetic network, reconstruction, simulated annealing, software.
Note: http://dx.doi.org/10.1093/molbev/msn066.
       
Toggle abstract
16
photophotophotophoto
Galina Glazko, Vladimir Makarenkov, Jing Liu and Arcady Mushegian. Evolutionary history of bacteriophages with double-stranded DNA genomes. In Biology Direct, Vol. 2(36), 2007.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, Program T REX.
Note: http://dx.doi.org/10.1186/1745-6150-2-36.
       
Toggle abstract
17
photophotophoto
Bin Ma, Lusheng Wang and Ming Li. Fixed topology alignment with recombination. In DAM, Vol. 104:281-300, 2000.
Keywords: approximation, explicit network, from network, from sequences, galled tree, inapproximability, phylogenetic network, phylogeny, recombination.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.40.7759.
       
Toggle abstract
18
photophoto
Sagi Snir and Tamir Tuller. The NET-HMM approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. In JBCB, Vol. 7(4):625-644, 2009.
Keywords: explicit network, from sequences, HMM, lateral gene transfer, likelihood, phylogenetic network, phylogeny, statistical model.
Note: http://research.haifa.ac.il/~ssagi/published%20papers/Snir-NET-HMM-JBCB-2009.pdf.
       
Toggle abstract
19
photophoto
Sarah C. Ayling and Terence A. Brown. Novel methodology for construction and pruning of quasi-median networks. In BMCB, Vol. 9:115, 2009.
Keywords: abstract network, from sequences, median network, phylogenetic network, phylogeny, quasi-median network, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2105-9-115.
       
Toggle abstract
20
photophotophoto
Tal Dagan, Yael Artzy-Randrup and William Martin. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. In PNAS, Vol. 105:10039-10044, 2008.
Keywords: from sequences, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1073/pnas.0800679105.
       
Toggle abstract
21
photo
Hans-Jürgen Bandelt and Arne Dür. Translating DNA data tables into quasi-median networks for parsimony analysis and error detection. In MPE, Vol. 42(1):256-271, 2007.
Keywords: abstract network, from sequences, parsimony, phylogenetic network, phylogeny, quasi-median network, reconstruction.
Note: http://dx.doi.org/10.1016/j.ympev.2006.07.013.
       
Toggle abstract
22
photophoto
Leo van Iersel and Steven Kelk. When two trees go to war. In JTB, Vol. 269(1):245-255, 2011.
Keywords: APX hard, explicit network, from clusters, from rooted trees, from sequences, from triplets, level k phylogenetic network, minimum number, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1004.5332.
       
Toggle abstract
23
photophotophoto
Hyun Jung Park, Guohua Jin and Luay Nakhleh. Bootstrap-based Support of HGT Inferred by Maximum Parsimony. In BMCEB, Vol. 10:131, 2010.
Keywords: bootstrap, explicit network, from sequences, lateral gene transfer, parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2148-10-131.
       
Toggle abstract
24
photophotophoto
Fumei Lam, Ryan Tarpine and Sorin Istrail. The Imperfect Ancestral Recombination Graph Reconstruction Problem: Upper Bounds for Recombination and Homoplasy. In JCB, Vol. 17(6), 2010.
Keywords: explicit network, from sequences, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.brown.edu/~sorin/pdfs/Lam%20the%20imperfect.pdf.
       

25
photophotophotophotophotophotophoto
Marta Melé, Asif Javed, Marc Pybus, Francesc Calafell, Laxmi Parida, Jaume Bertranpetit and Genographic Consortium. A New Method to Reconstruct Recombination Events at a Genomic Scale. In PLoS Computational Biology, Vol. 6(11):e1001010.1-13, 2010.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1371/journal.pcbi.1001010.
       
Toggle abstract
26
photophoto
Sagi Snir and Edward Trifonov. A Novel Technique for Detecting Putative Horizontal Gene Transfer in the Sequence Space. In JCB, Vol. 17(11):1535-1548, 2010.
Keywords: from sequences, phylogenetic network, phylogeny, reconstruction.
Note: http://research.haifa.ac.il/~ssagi/published%20papers/JCB-HGT.pdf.
       
Toggle abstract
27
photophoto
Alix Boc and Vladimir Makarenkov. Towards an accurate identification of mosaic genes and partial horizontal gene transfers. In NAR, Vol. 39(21):e144, 2011.
Keywords: explicit network, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction.
Note: http://dx.doi.org/10.1093/nar/gkr735.
       
Toggle abstract
28
photophoto
Lavanya Kannan and Ward C Wheeler. Maximum Parsimony on Phylogenetic Networks. In ALMOB, Vol. 7:9, 2012.
Keywords: dynamic programming, explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1186/1748-7188-7-9.
       
Toggle abstract
29
photophoto
Sven Herrmann and Vincent Moulton. Computing the blocks of a quasi-median graph. In DAM, Vol. 179:129-138, 2014.
Keywords: abstract network, from sequences, phylogenetic network, phylogeny, polynomial, Program QuasiDec, quasi-median network, reconstruction.
Note: http://arxiv.org/abs/1206.6135.
       

30
photophotophotophoto
Mareike Fischer, Leo van Iersel, Steven Kelk and Celine Scornavacca. On Computing The Maximum Parsimony Score Of A Phylogenetic Network. In SIDMA, Vol. 29(1):559-585, 2015.
Keywords: APX hard, cluster containment, explicit network, FPT, from network, from sequences, integer linear programming, level k phylogenetic network, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, Program MPNet, reconstruction, software.
Note: http://arxiv.org/abs/1302.2430.
       

31
photophoto
Lavanya Kannan and Ward C Wheeler. Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming. In JCB, Vol. 21(4):303-319, 2014.
Keywords: explicit network, exponential algorithm, from network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.
       
Toggle abstract
32
photophotophotophotophotophoto
Joel Sjöstrand, Ali Tofigh, Vincent Daubin, Lars Arvestad, Bengt Sennblad and Jens Lagergren. A Bayesian Method for Analyzing Lateral Gene Transfer. In Systematic Biology, Vol. 63(3):409-420, 2014.
Keywords: bayesian, duplication, from rooted trees, from sequences, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program JPrIME-DLTRS, reconstruction.
Note: http://dx.doi.org/10.1093/sysbio/syu007.
       

33
photophotophotophoto
Christopher Bryant, Mareike Fischer, Simone Linz and Charles Semple. On the Quirks of Maximum Parsimony and Likelihood on Phylogenetic Networks. In JTB, Vol. 417:100-108, 2017.
Keywords: explicit network, from sequences, likelihood, parsimony, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1505.06898.
       

34
photo
Ward C Wheeler. Phylogenetic network analysis as a parsimony optimization problem. In BMCB, Vol. 16(296):1-9, 2015.
Keywords: explicit network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1186/s12859-015-0675-0.
       

35
photophotophotophotophoto
Gergely J. Szöllösi, Adrián Arellano Davín, Eric Tannier, Vincent Daubin and Bastien Boussau. Genome-scale phylogenetic analysis finds extensive gene transfer among fungi. In Philosophical Transactions of the Royal Society of London B: Biological Sciences, Vol. 370(1678):1-11, 2015.
Keywords: duplication, from sequences, lateral gene transfer, loss, phylogenetic network, phylogeny, Program ALE, reconstruction.
Note: http://dx.doi.org/10.1098/rstb.2014.0335.
       

36
photophoto
Jessica W. Leigh and David Bryant. PopART: full-feature software for haplotype network construction. In Methods in Ecology and Evolution, Vol. 6(9):1110-1116, 2015.
Keywords: abstract network, from sequences, haplotype network, MedianJoining, phylogenetic network, phylogeny, population genetics, Program PopART, Program TCS, software.
Note: http://dx.doi.org/10.1111/2041-210X.12410.
       

37
photophotophotophotophoto
Julia Matsieva, Steven Kelk, Celine Scornavacca, Chris Whidden and Dan Gusfield. A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. In TCBB, Vol. 14(2):404-417, 2017.
Keywords: ARG, explicit network, from sequences, minimum number, phylogenetic network, phylogeny.
       

38
photophoto
Hussein A. Hejase and Kevin J. Liu. A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. Vol. 17(422):1-12, 2016.
Keywords: abstract network, evaluation, from sequences, phylogenetic network, phylogeny, Program PhyloNet, Program PhyloNetworks SNaQ, reconstruction, simulation, unicyclic network.
Note: http://dx.doi.org/10.1186/s12859-016-1277-1.
       

39
photophoto
Rinku Mathur and Neeru Adlakha. A graph theoretic model for prediction of reticulation events and phylogenetic networks for DNA sequences. In Egyptian Journal of Basic and Applied Sciences, Vol. 3(3):263-271, 2016.
Keywords: from sequences, phylogenetic network, phylogeny, Program T REX.
Note: http://dx.doi.org/10.1016/j.ejbas.2016.07.004.
       

40
photophotophotophoto
Steven Kelk, Fabio Pardi, Celine Scornavacca and Leo van Iersel. Finding the most parsimonious or likely tree in a network with respect to an alignment. In JOMB, Vol. 78:527-547, 2019.
Keywords: APX hard, from network, from sequences, likelihood, NP complete, parsimony.
Note: https://arxiv.org/abs/1707.03648.
       

41
photophotophoto
Claudia Solís-Lemus, Paul Bastide and Cécile Ané. PhyloNetworks: A Package for Phylogenetic Networks. In MBE, Vol. 34(12):3292-3298, 2017.
Keywords: from sequences, from trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, software.
Note: https://doi.org/10.1093/molbev/msx235.
       

42
photophotophoto
Leo van Iersel, Mark Jones and Celine Scornavacca. Improved maximum parsimony models for phylogenetic networks. In SB, Vol. 67(3):518-542, 2018.
Keywords: explicit network, FPT, from sequences, NP complete, parsimony, phylogenetic network, phylogeny, reconstruction, weakly displaying.
Note: https://leovaniersel.files.wordpress.com/2017/12/improved_parsimony_networks.pdf.
       

43
photophotophotophoto
Chi Zhang, Huw A. Ogilvie, Alexei J. Drummond and Tanja Stadler. Bayesian Inference of Species Networks from Multilocus Sequence Data. In MBE, Vol. 35(2):504-517, 2018.
Keywords: bayesian, explicit network, from sequences, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: https://dx.doi.org/10.1093/molbev/msx307.
       

44
photophoto
Dingqiao Wen and Luay Nakhleh. Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data. In SB, Vol. 67(3):439-457, 2018.
Keywords: bayesian, explicit network, from sequences, incomplete lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
Note: https://doi.org/10.1093/sysbio/syx085.
       

InProceedings
45
photophotophoto
Dan Gusfield, Satish Eddhu and Charles Langley. Efficient reconstruction of phylogenetic networks with constrained recombination. In CSB03, Pages 363-374, 2003.
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, recombination, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/ieeefinal.pdf.
       

46
photophoto
Dan Gusfield and Vikas Bansal. A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters. In RECOMB05, Vol. 3500:217-232 of LNCS, springer, 2005.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, polynomial, recombination, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/gusfieldrecomb.pdf.
       

47
photophoto
Daniel H. Huson and Tobias Kloepper. Computing recombination networks from binary sequences. In ECCB05, Vol. 21(suppl. 2):ii159-ii165 of BIO, 2005.
Keywords: from sequences, phylogenetic network, phylogeny, recombination.
Note: http://dx.doi.org/10.1093/bioinformatics/bti1126.
       
Toggle abstract
48
photophoto
John Kececioglu and Dan Gusfield. Reconstructing a history of recombinations from a set of sequences. In SODA94, Pages 471-480, 1994.
Keywords: from sequences, NP complete, polynomial, recombination, reconstruction.
Note: http://portal.acm.org/citation.cfm?id=314626#.
       

49
photophotophoto
Rune Lyngsø, Yun S. Song and Jotun Hein. Minimum Recombination Histories by Branch and Bound. In WABI05, Vol. 3692:239-250 of LNCS, springer, 2005.
Keywords: ARG, branch and bound, from sequences, minimum number, Program Beagle, recombination, reconstruction, software.
Note: http://www.cs.ucdavis.edu/~yssong/Pub/WABI05-239.pdf.
       

50
photophotophoto
Lusheng Wang, Kaizhong Zhang and Louxin Zhang. Perfect phylogenetic networks with recombination. In SAC01, Pages 46-50, 2001.
Keywords: from sequences, galled tree, NP complete, perfect, phylogenetic network, phylogeny, polynomial, recombination, reconstruction.
Note: http://dx.doi.org/10.1145/372202.372271.
       

51
photophoto
Sagi Snir and Tamir Tuller. Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. In WABI08, Vol. 5251:354-368 of LNCS, springer, 2008.
Keywords: explicit network, from sequences, HMM, lateral gene transfer, likelihood, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1007/978-3-540-87361-7_30.
       
Toggle abstract
52
photophoto
Ernst Althaus and Rouven Naujoks. Reconstructing Phylogenetic Networks with One Recombination. In Proceedings of the seventh International Workshop on Experimental Algorithms (WEA'08), Vol. 5038:275-288 of LNCS, springer, 2008.
Keywords: enumeration, explicit network, exponential algorithm, from sequences, generation, parsimony, phylogenetic network, phylogeny, reconstruction, unicyclic network.
Note: http://dx.doi.org/10.1007/978-3-540-68552-4_21.
       
Toggle abstract
53
photophotophoto
Cuong Than, Guohua Jin and Luay Nakhleh. Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. In Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'08), Vol. 5267:113-127 of LNCS, springer, 2008.
Keywords: bootstrap, explicit network, from rooted trees, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program Nepal, Program PhyloNet, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg-08.pdf, slides available at http://igm.univ-mlv.fr/RCG08/RCG08slides/Cuong_Than_RCG08.pdf.
       

54
photophotophoto
Bin Ma, Lusheng Wang and Ming Li. Fixed topology alignment with recombination. In CPM98, Vol. 1448:174-188 of LNCS, springer, 1998.
Keywords: approximation, explicit network, from network, from sequences, galled tree, inapproximability, phylogenetic network, phylogeny, recombination.
Note: http://dx.doi.org/10.1007/BFb0030789.
       

55
photophotophoto
Hadas Birin, Zohar Gal-Or, Isaac Elias and Tamir Tuller. Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion. In WABI07, Vol. 4645:111-123 of LNCS, springer, 2007.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, reconstruction.
Note: http://safrabio.cs.tau.ac.il/download/Papers/Birin_et_al.pdf.
       

56
photo
Wei-Shun Su, Tso-Ching Lee and Yaw-Ling Lin. Efficient Algorithms for Constructing Phylogenetic Networks with Restricted Recombinations. In NCS05, Pages 1-7, 2005.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, reconstruction.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.168.6735.
       

57
photo
Cayla McBee. Generalizing Fourier Calculus on Evolutionary Trees to Splits Networks. In ISPAN'12, Pages 149-155, 2012.
Keywords: abstract network, from sequences, phylogenetic network, phylogeny, split network, statistical model.
       
Toggle abstract
58
photophoto
Quan Nguyen and Teemu Roos. Likelihood-based inference of phylogenetic networks from sequence data by PhyloDAG. In AlCoB15, Vol. 9199:126-140 of LNCS, springer, 2015.
Keywords: BIC, explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software.
Note: http://www.cs.helsinki.fi/u/ttonteri/pub/alcob2015.pdf.
       

InBook
59
photo
Daniel H. Huson. Split networks and Reticulate Networks. In Olivier Gascuel and Mike Steel editors, Reconstructing Evolution, New Mathematical and Computational Advances, Pages 247-276, Oxford University Press, 2007.
Keywords: abstract network, consensus, from rooted trees, from sequences, from splits, from unrooted trees, galled tree, hybridization, phylogenetic network, phylogeny, Program Beagle, Program Spectronet, Program SplitsTree, Program SPNet, recombination, reconstruction, split network, survey.
Note: similar to http://www-ab.informatik.uni-tuebingen.de/research/phylonets/GCB2006.pdf.
       

60
photophoto
Guillaume Bourque and Louxin Zhang. Models and Methods in Comparative Genomics. In Chau-Wen Tseng editor, Advances in Computers, Special Volume: Computational Biology, Vol. 68, Elsevier, 2006.
Keywords: from distances, from rooted trees, from sequences, galled tree, phylogenetic network, phylogeny, survey.
Note: http://www.math.nus.edu.sg/~matzlx/papers/CompGen_ZLX.pdf.
       

PhdThesis
61
photo
Tobias Kloepper. Algorithms for the Calculation and Visualisation of Phylogenetic Networks. PhD thesis, Eberhard-Karls-Universität Tübingen, Germany, 2008.
Keywords: from rooted trees, from sequences, from unrooted trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization.
Note: https://publikationen.uni-tuebingen.de/xmlui/handle/10900/49159.
       

62
photo
Cuong Than. Inference of parsimonious species phylogenies from multi-locus data. PhD thesis, Rice University, U.S.A., 2010.
Keywords: explicit network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: http://hdl.handle.net/1911/62177.
       

63
photo
Rosalba Radice. A Bayesian Approach to Phylogenetic Networks. PhD thesis, University of Bath, U.K., 2011.
Keywords: bayesian, explicit network, from sequences, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://opus.bath.ac.uk/25521/.
       

64
photo
Yi-Chieh Wu. Computational evolutionary genomics : phylogenomic models spanning domains, genes, individuals, and species. PhD thesis, Massachusetts Institute of Technology, U.S.A., 2014.
Keywords: duplication, from sequences, from species tree, lateral gene transfer, loss, phylogeny, Program TreeFix-DTL, reconstruction.
Note: http://hdl.handle.net/1721.1/87937.
       

Misc
65
photo
Dan Gusfield. On the Full-Decomposition Optimality Conjecture for Phylogenetic Networks. 2005.
Keywords: characterization, explicit network, from sequences, phylogenetic network, reconstruction.
Note: UC Davis Computer Science Technical Report CSE-2005, http://wwwcsif.cs.ucdavis.edu/~gusfield/fullydecomp.pdf.
       

66
photo
Cécile Ané. From reconstructing to using phylogenetic networks. Phyloseminar #72, 2017.
Keywords: explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, semidirected network.
Note: https://www.youtube.com/watch?v=PF4j_JOQP0c.