TY - CHAP AU - Wagner, W. H. ED - Platnick, N. I. ED - Funk, V. A. PY - 1983 DA - 1983// TI - Reticulistics: the recognition of hybrids and their role in cladistics and classification BT - Advances in Cladistics PB - Columbia University Press CY - New York ID - Wagner1983 ER - TY - JOUR AU - Syvanen, M. PY - 1985 DA - 1985// TI - Cross-species gene transfer; implications for a new theory of evolution JO - J Theor Biol VL - 112 UR - https://doi.org/10.1016/S0022-5193(85)80291-5 DO - 10.1016/S0022-5193(85)80291-5 ID - Syvanen1985 ER - TY - JOUR AU - Smith, G. J. AU - Vijaykrishna, D. AU - Bahl, J. AU - Lycett, S. J. AU - Worobey, M. AU - Pybus, O. G. PY - 2009 DA - 2009// TI - Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic JO - Nature VL - 459 UR - https://doi.org/10.1038/nature08182 DO - 10.1038/nature08182 ID - Smith2009 ER - TY - JOUR AU - Lankester, E. R. PY - 1870 DA - 1870// TI - On the use of the term homology in modern zoology, and the distinction between homogenetic and homoplastic agreements JO - Ann Mag Nat Hist Zool Bot Geol VL - 6 ID - Lankester1870 ER - TY - BOOK AU - Gusfield, D. PY - 1997 DA - 1997// TI - Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology PB - Cambridge University Press CY - Cambridge UR - https://doi.org/10.1017/CBO9780511574931 DO - 10.1017/CBO9780511574931 ID - Gusfield1997 ER - TY - JOUR AU - Dikow, R. PY - 2011 DA - 2011// TI - Genome-level homology and phylogeny of Shewanella (Gammaproteobacteria: lteromonadales: Shewanellaceae) JO - BMC Genomics VL - 12 UR - https://doi.org/10.1186/1471-2164-12-237 DO - 10.1186/1471-2164-12-237 ID - Dikow2011 ER - TY - JOUR AU - Huson, D. H. AU - Scornavacca, C. PY - 2011 DA - 2011// TI - A survey of combinatorial methods for phylogenetic networks JO - Genome Biol Evol VL - 3 UR - https://doi.org/10.1093/gbe/evq077 DO - 10.1093/gbe/evq077 ID - Huson2011 ER - TY - BOOK AU - Huson, D. H. AU - Rupp, R. AU - Scornavacca, C. PY - 2011 DA - 2011// TI - Phylogenet Netw PB - Cambridge University Press CY - Cambridge, UK ID - Huson2011 ER - TY - JOUR AU - Bandelt, H. J. AU - Dress, A. W. M. PY - 1992 DA - 1992// TI - A canonical decomposition theory for metrics on a finite set JO - Adv Math VL - 92 UR - https://doi.org/10.1016/0001-8708(92)90061-O DO - 10.1016/0001-8708(92)90061-O ID - Bandelt1992 ER - TY - JOUR AU - Bokhari, S. AU - Pomeroy, L. AU - Janies, D. PY - 2010 DA - 2010// TI - Reassortment Networks and the Evolution of Pandemic H1N1 Swine-origin Influenza JO - IEEE Trans Comput Biol Bioinformatics VL - 9 UR - https://doi.org/10.1109/TCBB.2011.95 DO - 10.1109/TCBB.2011.95 ID - Bokhari2010 ER - TY - JOUR AU - Bokhari, S. AU - Janies, D. PY - 2012 DA - 2012// TI - Reassortment Networks for Investigating the Evolution of Segmented Viruses JO - IEEE Trans Comput Biol Bioinformatic VL - 12 ID - Bokhari2012 ER - TY - CHAP AU - Huson, D. H. AU - Rupp, R. ED - Crandall, K. ED - Lagergren, J. PY - 2008 DA - 2008// TI - Summarizing multiple gene trees using cluster networks BT - Algorithms in Bioinformatics PB - Springer CY - Berlin, DE ID - Huson2008 ER - TY - JOUR AU - Moret, B. M. E. AU - Nakhleh, L. AU - Warnow, T. AU - Linder, C. R. AU - Tholse, A. AU - Padolina, A. PY - 2004 DA - 2004// TI - Phylogenetic networks: Modeling, reconstructibility, and accuracy JO - IEEE Trans Comput Biol Bioinformatics VL - 1 UR - https://doi.org/10.1109/TCBB.2004.10 DO - 10.1109/TCBB.2004.10 ID - Moret2004 ER - TY - JOUR AU - Strimmer, K. AU - Moulton, V. PY - 2000 DA - 2000// TI - Likelihood analysis of phylogenetic networks using directed graphical models JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026367 DO - 10.1093/oxfordjournals.molbev.a026367 ID - Strimmer2000 ER - TY - JOUR AU - Jin, G. AU - Nakhleh, L. AU - Snir, S. AU - Tuller, T. PY - 2006 DA - 2006// TI - Maximum likelihood of phylogenetic networks JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl452 DO - 10.1093/bioinformatics/btl452 ID - Jin2006 ER - TY - BOOK AU - Wheeler, W. C. PY - 2012 DA - 2012// TI - Systematics: A Course of Lectures PB - Wiley-Blackwell CY - Oxford, UK UR - https://doi.org/10.1002/9781118301081 DO - 10.1002/9781118301081 ID - Wheeler2012 ER - TY - JOUR AU - Cordue, P. AU - Linz, S. AU - Semple, C. PY - 2014 DA - 2014// TI - Phylogenetic networks that display a tree twice JO - Bull Math Biol VL - 76 UR - https://doi.org/10.1007/s11538-014-0032-x DO - 10.1007/s11538-014-0032-x ID - Cordue2014 ER - TY - JOUR AU - Hein, J. PY - 1990 DA - 1990// TI - Recontructing evolution of sequences subject to recombination unsing parsimony JO - Math Biosci VL - 98 UR - https://doi.org/10.1016/0025-5564(90)90123-G DO - 10.1016/0025-5564(90)90123-G ID - Hein1990 ER - TY - JOUR AU - Hein, J. PY - 1993 DA - 1993// TI - A heuristic method to reconstruct the history of sequences subject to recombination JO - J Mol Evol VL - 36 UR - https://doi.org/10.1007/BF00182187 DO - 10.1007/BF00182187 ID - Hein1993 ER - TY - STD TI - Nakhleh L, Jin G, Zhao F, Mellor-Crummey J. Reconstructing phylogenetic networks using parsimony In: Marstein V, editor. Proceeding of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB’05): 2005. p. 93–102. ID - ref20 ER - TY - JOUR AU - Kannan, L. AU - Wheeler, W. C. PY - 2012 DA - 2012// TI - Maximum parsimony on phylogenetic networks JO - Algorithms Mol Biol VL - 7 UR - https://doi.org/10.1186/1748-7188-7-9 DO - 10.1186/1748-7188-7-9 ID - Kannan2012 ER - TY - JOUR AU - Kannan, L. AU - Wheeler, W. C. PY - 2014 DA - 2014// TI - Exactly computing the parsimony scores on phylogenetic networks using dynamic programming JO - J Comput Biol VL - 21 UR - https://doi.org/10.1089/cmb.2013.0134 DO - 10.1089/cmb.2013.0134 ID - Kannan2014 ER - TY - JOUR AU - Fitch, W. M. PY - 1971 DA - 1971// TI - Toward defining the course of evolution: minimum change for a specific tree topology JO - Syst Zool VL - 20 UR - https://doi.org/10.2307/2412116 DO - 10.2307/2412116 ID - Fitch1971 ER - TY - STD TI - Fischer M, van Iersel L, Kelk S, Scornavacca C. SRAM Journal on Discrete Mathematics. 2013; 29:559–585. ID - ref24 ER - TY - JOUR AU - Wheeler, W. C. PY - 1993 DA - 1993// TI - The triangle inequality and character analysis JO - Mol Biol Evol VL - 10 ID - Wheeler1993 ER - TY - JOUR AU - Peloso, P. L. V. AU - Frost, D. R. AU - Richards, S. J. AU - Rodrigues, M. T. AU - Donnellan, S. AU - Matsui, M. PY - 2015 DA - 2015// TI - The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow-mouthed frogs (Anura, Microhylidae) JO - Cladistics VL - 31 UR - https://doi.org/10.1111/cla.12069 DO - 10.1111/cla.12069 ID - Peloso2015 ER - TY - JOUR AU - Wheeler, W. C. AU - Whiteley, P. M. PY - 2014 DA - 2014// TI - Historical linguistics as a sequence optimization problem: The evolution and biogeography of Uto-Aztecan languages JO - Cladistics VL - 31 UR - https://doi.org/10.1111/cla.12078 DO - 10.1111/cla.12078 ID - Wheeler2014 ER - TY - BOOK AU - Swadesh, M. PY - 1971 DA - 1971// TI - The Origin and Diversification of Language PB - Aldine CY - Chicago ID - Swadesh1971 ER - TY - STD TI - Wheeler WC, Lucaroni N, Hong L, Crowley LM, Varón A. POY version 5.0. American Museum of Natural History. 2013. http://research.amnh.org/scicomp/projects/poy.php. UR - http://research.amnh.org/scicomp/projects/poy.php ID - ref29 ER - TY - JOUR AU - Wheeler, W. C. AU - Lucaroni, N. AU - Hong, L. AU - Crowley, L. M. AU - Varón, A. PY - 2015 DA - 2015// TI - POY version 5: Phylogenetic analysis using dynamic homologies under multiple optimality criteria JO - Cladistics VL - 31 UR - https://doi.org/10.1111/cla.12083 DO - 10.1111/cla.12083 ID - Wheeler2015 ER - TY - JOUR AU - Moilanen, A. PY - 1999 DA - 1999// TI - Searching for most parsimonious trees with simulated evolutionary optimization JO - Cladistics VL - 15 UR - https://doi.org/10.1111/j.1096-0031.1999.tb00393.x DO - 10.1111/j.1096-0031.1999.tb00393.x ID - Moilanen1999 ER - TY - JOUR AU - Goloboff, P. PY - 1999 DA - 1999// TI - Analyzing large data sets in reasonable times: solutions for composite optima JO - Cladistics VL - 15 UR - https://doi.org/10.1111/j.1096-0031.1999.tb00278.x DO - 10.1111/j.1096-0031.1999.tb00278.x ID - Goloboff1999 ER - TY - JOUR AU - Huson, D. H. AU - Scornavacca, C. PY - 2012 DA - 2012// TI - Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks JO - Syst Biol. VL - 61 UR - https://doi.org/10.1093/sysbio/sys062 DO - 10.1093/sysbio/sys062 ID - Huson2012 ER - TY - STD TI - Cardona G, Russelló F, Valiente G. Extended newick: it is time for a standard representation of phylogenetic networks. BMC Bioinformatics. 2008; 9(532). doi:10.1186/1471-2105-9-532. UR - http://dx.doi.org/10.1186/1471-2105-9-532 ID - ref34 ER - TY - STD TI - Hill KC. Wick Miller’s Uto-Aztecan Cognate Sets, Revised and expanded by Kenneth C. 2011. ID - ref35 ER - TY - JOUR AU - Cartwright, R. A. PY - 2005 DA - 2005// TI - DNA assembly with gaps (DAWG): simulating sequence evolution JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1200 DO - 10.1093/bioinformatics/bti1200 ID - Cartwright2005 ER - TY - JOUR AU - Tavaré, S. PY - 1986 DA - 1986// TI - Some probabilistic and statistical problems on the analysis of DNA sequences JO - Lec Math Life Sci VL - 17 ID - Tavaré1986 ER - TY - JOUR AU - Yang, Z. PY - 1994 DA - 1994// TI - Maximum likelihood phylogeentic estimation from DNA sequences withvariable rates over sites: approximate methods JO - J Mol Evol VL - 39 UR - https://doi.org/10.1007/BF00160154 DO - 10.1007/BF00160154 ID - Yang1994 ER -