Australian Systematic Botany Australian Systematic Botany Society
Taxonomy, biogeography and evolution of plants

Articles citing this paper

Multiple sequence alignment for phylogenetic purposes

David A. Morrison

Department of Parasitology (SWEPAR), National Veterinary Institute and Swedish University of Agricultural Sciences, 751 89 Uppsala, Sweden. Email: David.Morrison@bvf.slu.se

Australian Systematic Botany 19(6) 479-539 https://doi.org/10.1071/SB06020
Submitted: 3 July 2006  Accepted: 30 October 2006   Published: 14 December 2006



54 articles found in CrossRef database.

Delimitation of Ophiostoma quercus and its synonyms using multiple gene phylogenies
Grobbelaar Joha W., Aghayeva Dilzara N., de Beer Z. Wilhelm, Bloomer Paulette, Wingfield Michael J., Wingfield Brenda D.
Mycological Progress. 2009 8(3). p.221
Sequence characteristics and phylogenetic implications of the nrDNA internal transcribed spacers (ITS) in the genus Nymphaea with focus on some Indian representatives
Dkhar Jeremy, Kumaria Suman, Rao Satyawada Rama, Tandon Pramod
Plant Systematics and Evolution. 2012 298(1). p.93
Phylogenetic analyses of morphological evolution in the gametophyte and sporophyte generations of the moss order Hookeriales (Bryopsida)
Pokorny L., Ho B.-C., Frahm J.-P., Quandt D., Shaw A.J.
Molecular Phylogenetics and Evolution. 2012 63(2). p.351
Higher level phylogenetic relationships within the bamboos (Poaceae: Bambusoideae) based on five plastid markers
Kelchner Scot A.
Molecular Phylogenetics and Evolution. 2013 67(2). p.404
MOLECULAR EVIDENCE CONFIRMS SISTER RELATIONSHIP OFARDISSONEA,CLIMACOSPHENIA,ANDTOXARIUMWITHIN THE BIPOLAR CENTRIC DIATOMS (BACILLARIOPHYTA, MEDIOPHYCEAE), AND CLADISTIC ANALYSES CONFIRM THAT EXTREMELY ELONGATED SHAPE HAS ARISEN TWICE IN THE DIATOMS1
Medlin Linda K., Sato Shinya, Mann David G., Kooistra Wiebe H. C. F.
Journal of Phycology. 2008 44(5). p.1340
A molecular phylogeny of the Lepidozia generic complex supports re-circumscription of the Lepidozioideae
Cooper Endymion D., Henwood Murray J., Brown Elizabeth A.
Molecular Phylogenetics and Evolution. 2012 65(1). p.10
Phylogeny and evolution of the Meliphagoidea, the largest radiation of Australasian songbirds
Gardner Janet L., Trueman John W.H., Ebert Daniel, Joseph Leo, Magrath Robert D.
Molecular Phylogenetics and Evolution. 2010 55(3). p.1087
Systematics and ecology of the Australasian genus Empodisma (Restionaceae) and description of a new species from peatlands in northern New Zealand
Wagstaff Steven, Clarkson Beverly
PhytoKeys. 2012 13(0). p.39
Genetics and Evolution of Infectious Diseases (2017)
Morrison D.A.
Evolution of the Apicomplexa: where are we now?
Morrison David A.
Trends in Parasitology. 2009 25(8). p.375
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment
Wright Erik S.
BMC Bioinformatics. 2015 16(1).
Homology in coding and non-coding DNA sequences: a parsimony perspective
Ochoterena Helga
Plant Systematics and Evolution. 2009 282(3-4). p.151
Combining conservative and variable markers to infer the evolutionary history of Prunus subgen. Amygdalus s.l. under domestication
Delplancke Malou, Yazbek Mariana, Arrigo Nils, Espíndola Anahí, Joly Helene, Alvarez Nadir
Genetic Resources and Crop Evolution. 2016 63(2). p.221
DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS
Subramanian A. R., Hiran S., Steinkamp R., Meinicke P., Corel E., Morgenstern B.
Nucleic Acids Research. 2010 38(Web Server). p.W19
Genetic differences in internal transcribed spacer 1 between Dermanyssus gallinae from wild birds and domestic chickens
BRÄNNSTRÖM S., MORRISON D. A., MATTSSON J. G., CHIRICO J.
Medical and Veterinary Entomology. 2008 22(2). p.152
Sequencing and Phylogenetic Analysis of Potato virus Y Liaoning Isolate in China
WANG Fang, GAO Zheng-liang, AN Meng-nan, ZHOU Ben-guo, WU Yuan-hua
Journal of Integrative Agriculture. 2013 12(7). p.1195
Interspecific variation in mitochondrial serine transfer RNA (UCN) in Euptychiina butterflies (Lepidoptera: Satyrinae): Structure and alignment
Marín Mario Alejandro, López Andrés, Uribe Sandra Inés
Mitochondrial DNA. 2012 23(3). p.208
Molecular evolution and diversification of the moss family Daltoniaceae (Hookeriales, Bryophyta) with emphasis on the unravelling of the phylogeny of Distichophyllum and its allies
Ho Boon-Chuan, Pokorny Lisa, Tan Benito C., Frahm Jan-Peter, Shaw A. Jonathan, Quandt Dietmar
Botanical Journal of the Linnean Society. 2012 170(2). p.157
Phylogenetics and phylogeography of the monocot genus Baldellia (Alismataceae): Mediterranean refugia, suture zones and implications for conservation
Arrigo Nils, Buerki Sven, Sarr Anouk, Guadagnuolo Roberto, Kozlowski Gregor
Molecular Phylogenetics and Evolution. 2011 58(1). p.33
Secondary structure alignment and direct optimization of 28S rDNA sequences provide limited phylogenetic resolution in bark and ambrosia beetles (Curculionidae: Scolytinae)
Jordal Bjarte, Gillespie Joseph J., Cognato Anthony I.
Zoologica Scripta. 2007 0(0). p.071012014054001
The Muscoidea (Diptera: Calyptratae) are paraphyletic: Evidence from four mitochondrial and four nuclear genes
Kutty Sujatha Narayanan, Pape Thomas, Pont Adrian, Wiegmann Brian M., Meier Rudolf
Molecular Phylogenetics and Evolution. 2008 49(2). p.639
Phylogenetic models and model selection for noncoding DNA
Kelchner Scot A.
Plant Systematics and Evolution. 2009 282(3-4). p.109
Causes, consequences and solutions of phylogenetic incongruence
Som A.
Briefings in Bioinformatics. 2015 16(3). p.536
Phylogeny of the bristle worm family Eunicidae (Eunicida, Annelida) and the phylogenetic utility of noncongruent 16S, COI and 18S in combined analyses
Zanol Joana, Halanych Kenneth M., Struck Torsten H., Fauchald Kristian
Molecular Phylogenetics and Evolution. 2010 55(2). p.660
Monophyly of the ring-forming group in Diplopoda (Myriapoda, Arthropoda) based on SSU and LSU ribosomal RNA sequences
Cong Peiyun, Xia Xuhua, Yang Qun
Progress in Natural Science. 2009 19(10). p.1297
Genetic structure and evolution of Alpine polyploid complexes:Ranunculus kuepferi(Ranunculaceae) as a case study
BURNIER J., BUERKI S., ARRIGO N., KÜPFER P., ALVAREZ N.
Molecular Ecology. 2009 18(17). p.3730
A reality check for alignments and trees
Martin William, Roettger Mayo, Lockhart Peter J.
Trends in Genetics. 2007 23(10). p.478
Phylogeography of Ostreopsis along West Pacific Coast, with Special Reference to a Novel Clade from Japan
Sato Shinya, Nishimura Tomohiro, Uehara Keita, Sakanari Hiroshi, Tawong Wittaya, Hariganeya Naohito, Smith Kirsty, Rhodes Lesley, Yasumoto Takeshi, Taira Yosuke, Suda Shoichiro, Yamaguchi Haruo, Adachi Masao, Neilan Brett
PLoS ONE. 2011 6(12). p.e27983
Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora)
Luan Peng-tao, Ryder Oliver A., Davis Heidi, Zhang Ya-ping, Yu Li
Molecular Phylogenetics and Evolution. 2013 66(3). p.748
Malagasy Dracaena Vand. ex L. (Ruscaceae): an investigation of discrepancies between morphological features and spatial genetic structure at a small evolutionary scale
Buerki Sven, Callmander Martin W., Schüpfer Fanny, Ravokatra Mamy, Küpfer Philippe, Alvarez Nadir
Plant Systematics and Evolution. 2009 280(1-2). p.15
Plastid and nuclear DNA markers reveal intricate relationships at subfamilial and tribal levels in the soapberry family (Sapindaceae)
Buerki Sven, Forest Félix, Acevedo-Rodríguez Pedro, Callmander Martin W., Nylander Johan A.A., Harrington Mark, Sanmartín Isabel, Küpfer Philippe, Alvarez Nadir
Molecular Phylogenetics and Evolution. 2009 51(2). p.238
Bayesian Phylogenetic Inference Using a Combinatorial Sequential Monte Carlo Method
Wang Liangliang, Bouchard-Côté Alexandre, Doucet Arnaud
Journal of the American Statistical Association. 2015 110(512). p.1362
Warneckea parvifolia (Melastomataceae–Olisbeoideae), a new “sand-forest” endemic from northeastern KwaZulu-Natal (South Africa) and southernmost Mozambique, and a phylogenetic analysis of eastern and southern African representatives of W. section Warneckea
Stone R.D., Ntetha N.A.
South African Journal of Botany. 2013 88 p.317
Structural alignment of 18S and 28S rDNA sequences provides insights into phylogeny of Phytophaga (Coleoptera: Curculionoidea and Chrysomeloidea)
Marvaldi Adriana E., Duckett Catherine N., Kjer Karl M., Gillespie Joseph J.
Zoologica Scripta. 2009 38(1). p.63
Evolutionary History and Population Dynamics of Hepatitis E Virus
Purdy Michael A., Khudyakov Yury E., Tavis John E.
PLoS ONE. 2010 5(12). p.e14376
New records, replacements, reinstatements and four new species in the Radula parvitexta and R. ventricosa species groups (Jungermanniopsida) in Australia: cases of mistaken identity
Renner Matt A. M., Devos Nicolas, Brown Elizabeth A., von Konrat Matt J.
Australian Systematic Botany. 2013 26(4). p.298
Inference of molecular homology and sequence alignment by direct optimization
Morgan Matthew J., Kelchner Scot A.
Molecular Phylogenetics and Evolution. 2010 56(1). p.305
Genomic Analysis of the Natural Population of Wheat dwarf virus in Wheat from China and Hungary
LIU Yan, WANG Biao, Vida Gyula, Cséplo-Károlyi Mónika, WU Bei-lei, WU Yuan-hua, WANG Xi-feng
Journal of Integrative Agriculture. 2012 11(12). p.2020
The deterministic effects of alignment bias in phylogenetic inference
Simmons Mark P., Müller Kai F., Webb Colleen T.
Cladistics. 2011 27(4). p.402
New World Origins of Southwest Pacific Gesneriaceae: Multiple Movements Across and Within the South Pacific
Woo Vincent L., Funke Minde M., Smith James F., Lockhart Peter J., Garnock-Jones Philip J.
International Journal of Plant Sciences. 2011 172(3). p.434
The genera Chiastocaulon, Cryptoplagiochila and Pedinophyllum (Plagiochilaceae) in Australia
Renner Matt A. M., Heslewood Margaret M., Patzak Simon D. F., Sch�fer-Verwimp Alfons, Heinrichs Jochen
Australian Systematic Botany. 2016 29(5). p.358
A min-cut algorithm for the consistency problem in multiple sequence alignment
Corel E., Pitschi F., Morgenstern B.
Bioinformatics. 2010 26(8). p.1015
A framework for phylogenetic sequence alignment
Morrison David A.
Plant Systematics and Evolution. 2009 282(3-4). p.127
Molecular homology and multiple-sequence alignment: an analysis of concepts and practice
Morrison David A., Morgan Matthew J., Kelchner Scot A.
Australian Systematic Botany. 2015 28(1). p.46
Molecular phylogeny of the arthrostylidioid bamboos (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae) and new genus Didymogonyx
Tyrrell Christopher D., Santos-Gonçalves Ana Paula, Londoño Ximena, Clark Lynn G.
Molecular Phylogenetics and Evolution. 2012 65(1). p.136
Ultra-large alignments using phylogeny-aware profiles
Nguyen Nam-phuong D., Mirarab Siavash, Kumar Keerthana, Warnow Tandy
Genome Biology. 2015 16(1).
Non-coding nuclear DNA markers in phylogenetic reconstruction
Calonje Miriam, Martín-Bravo Santiago, Dobeš Christoph, Gong Wei, Jordon-Thaden Ingrid, Kiefer Christiane, Kiefer Markus, Paule Juraj, Schmickl Roswitha, Koch Marcus A.
Plant Systematics and Evolution. 2009 282(3-4). p.257
Cleaning wrasse species vary with respect to dependency on the mutualism and behavioural adaptations in interactions
Barbu Lise, Guinand Christelle, Bergmüller Ralph, Alvarez Nadir, Bshary Redouan
Animal Behaviour. 2011 82(5). p.1067
Direct optimization overly optimizes data
YOSHIZAWA KAZUNORI
Systematic Entomology. 2010 35(2). p.199
The molecular phylogeny of freshwater Dothideomycetes
Shearer C.A., Raja H.A., Miller A.N., Nelson P., Tanaka K., Hirayama K., Marvanová L., Hyde K.D., Zhang Y.
Studies in Mycology. 2009 64 p.145
Genetics and Evolution of Infectious Disease (2011)
Morrison David A.
An application of dynamic homology to morphological characters: direct optimization of setae sequences and phylogeny of the family Odontellidae (Poduromorpha, Collembola)
Agolin Mikaël, D’Haese Cyrille A.
Cladistics. 2009 25(4). p.353
Behaviour and Physiology of Root Herbivores (2013)
Hiltpold Ivan, Bernklau Elisa, Bjostad Louis B., Alvarez Nadir, Miller-Struttmann Nicole E., Lundgren Jonathan G., Hibbard Bruce E.
Abstract Full Text PDF (971 KB) Export Citation