SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information
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Ang, 2008, Secondarily reduced foreleg armature in Perochaeta dikowi sp.n. (Diptera: Cyclorrhapha: Sepsidae) due to a novel mounting technique, Syst. Entomol., 33, 552, 10.1111/j.1365-3113.2008.00422.x
Balke, 2009, New Guinea highland origin of a widespread arthropod supertramp, Proc. R. Soc. Lond. B Biol. Sci., 276, 2359, 10.1098/rspb.2009.0015
Dunn, 2008, Broad phylogenomic sampling improves resolution of the animal tree of life, Nature, 452, 745, 10.1038/nature06614
Goloboff, 2008, TNT, a free program for phylogenetic analysis, Cladistics, 24, 774, 10.1111/j.1096-0031.2008.00217.x
Huang, 2009, More evidence for pervasive paraphyly in scleractinian corals: systematic study of Southeast Asian Faviidae (Cnidaria; Scleractinia) based on molecular and morphological data, Mol. Phylogenet. Evol., 50, 102, 10.1016/j.ympev.2008.10.012
Jones, 2006, TaxMan: a taxonomic database manager, BMC Bioinformatics, 7, 536, 10.1186/1471-2105-7-536
Kutty, 2007, Sensitivity analysis, molecular systematics and natural history evolution of Scathophagidae (Diptera: Cyclorrhapha: Calyptratae), Cladistics, 23, 64, 10.1111/j.1096-0031.2006.00131.x
Kutty, 2008, The Muscoidea (Diptera: Calyptratae) are paraphyletic: evidence from four mitochondrial and four nuclear genes, Mol. Phylogenet. Evol., 49, 639, 10.1016/j.ympev.2008.08.012
Kutty, 2010, Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine”s Fly, Syst. Entomol., 10.1111/j.1365-3113.2010.00536.x
Laamanen, 2005, Phylogenetic analysis of Themira (Sepsidae: Diptera): sensitivity analysis, alignment, and indel treatment in a multigene study, Cladistics, 21, 258, 10.1111/j.1096-0031.2005.00066.x
Lim, 2010, Mitochondrial and nuclear markers support the monophyly of Dolichopodidae and suggest a rapid origin of the subfamilies (Diptera: Empidoidea), Syst. Entomol., 35, 59, 10.1111/j.1365-3113.2009.00481.x
Lohman, 2008, Phylogeography and genetic diversity of a widespread Old World butterfly, Lampides boeticus (Lepidoptera: Lycaenidae), BMC Evol. Biol., 8, 301, 10.1186/1471-2148-8-301
Lohman, 2010, Cryptic genetic diversity in “widespread” Southeast Asian bird species suggests that Philippine avian endemism is gravely underestimated, Biol. Conserv., 143, 1885, 10.1016/j.biocon.2010.04.042
Maddison, 2001, MacClade 4: Analysis of Phylogeny and Character Evolution
Maddison , W.P. Maddison , D.R. 2009 Mesquite: a modular system for evolutionary analysis. Version 2.72 http://mesquiteproject.org
Maddison, 1997, NEXUS: an extensible file format for systematic information, Syst. Biol., 46, 590, 10.1093/sysbio/46.4.590
Meier, 2002, A cladistic analysis of Diopsidae (Diptera) based on morphological and DNA sequence data, Insect Syst. Evol., 33, 325, 10.1163/187631202X00181
Meier, 2002, A phylogenetic analysis of Coelopidae (Diptera) based on morphological and DNA sequence data, Mol. Phylogenet. Evol., 25, 393, 10.1016/S1055-7903(02)00276-2
Meier, 2006, DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success, Syst. Biol., 55, 715, 10.1080/10635150600969864
Meier, 2008, The use of mean instead of smallest interspecific distances exaggerates the size of the “barcoding gap” and leads to misidentification, Syst. Biol., 57, 809, 10.1080/10635150802406343
Nixon, 1992, Extinction and the origin of species, Extinction and Phylogeny, 117
Petersen, 2007, The phylogeny and evolution of host choice in the Hippoboscoidea (Diptera) as reconstructed using four molecular markers, Mol. Phylogenet. Evol., 45, 111, 10.1016/j.ympev.2007.04.023
Puniamoorthy, 2008, Bending for love: losses and gains of sexual dimorphisms are strictly correlated with changes in the mounting position of sepsid flies (Sepsidae: Diptera), BMC Evol. Biol., 8, 155, 10.1186/1471-2148-8-155
Puniamoorthy, 2009, From kissing to belly stridulation: comparative analysis reveals surprising diversity, rapid evolution, and much homoplasy in the mating behaviour of 27 species of sepsid flies (Diptera: Sepsidae), J. Evol. Biol., 22, 2146, 10.1111/j.1420-9101.2009.01826.x
Roure, 2007, SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics, BMC Evol. Biol., 7, 10.1186/1471-2148-7-S1-S2
Smith, 2008, Phyutility: a phyloinformatics tool for trees, alignments and molecular data, Bioinformatics, 24, 715, 10.1093/bioinformatics/btm619
Su, 2007, Convergent evolution of eye ultrastructure and divergent evolution of vision-mediated predatory behaviour in jumping spiders, J. Evol. Biol., 20, 1478, 10.1111/j.1420-9101.2007.01335.x
Su, 2008, Morphology versus molecules: the phylogenetic relationships of Sepsidae (Diptera: Cyclorrhapha) based on morphology and DNA sequence data from ten genes, Cladistics, 24, 902, 10.1111/j.1096-0031.2008.00222.x
Swofford, 2004, PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods)
Wowor, 2009, Evolution of life history traits in Asian freshwater prawns of the genus Macrobrachium (Crustacea: Decapoda: Palaemonidae) based on multilocus molecular phylogenetic analysis, Mol. Phylogenet. Evol., 52, 340, 10.1016/j.ympev.2009.01.002