Latest update: June 28 2010
Johan Nylander - Download page
@: Johan.Nylander-at-abc-dot-se
Programs/Scripts/Code
MrAIC v. 1.4.4. Perl script for selecting DNA substitution models using PHYML. README. [WIN/MACOSX/UNIX]
MrModeltest2 v. 2.3. C program for selecting DNA substitution models using PAUP*. README [WIN/MACOSX/UNIX]
Burntrees v. 0.1.7. Perl script for manipulating MrBayes tree and parameter files. The script comes with an extra tool, catmb.pl, for concatenating files from separate MrBayes runs. README. [WIN/MACOSX/UNIX]
Mailfit v. 0.2. Perl script that runs PAUP and MrModeltest2 (or Modeltest) and sends (optionally) results via e-mail. README [WIN/MACOSX/UNIX]
MrModelfit/Modelfit v. 1.2/1.2. Perl script for running MrModeltest2/Modeltest. README. [WIN/MACOSX/UNIX]
Vim Nexus syntax highlighting. Nexus syntax highlighting files for the Vim editor. Recognizes many/most of the PAUP/MrBayes commands. SCREENSHOT. [WIN/MACOSX/UNIX]
Vim Alignment highlighting. Vim highlighting files for DNA sequence alignments. SCREENSHOT. [WIN/MACOSX/UNIX]
Vim tips for phylo data. A small collection of scripts for working with phylo data in Vim/gVim. vim-phylo.vim. Demo movie (screen capture in FLV format, no sound) on using vim-phylo.
Bayes-DIVA analysis. Script and DIVA program used for the Bayes-DIVA analysis in Nylander et al. 2008. README.
Links to software on other pages
AWTY. Program for phylogenetic MCMC diagnostics. [Link to web server at FSU]
APE. Analysis of Phylogeny and Evolution using R. [Link to APE home page]
DIVA. Dispersal-Vicariance analysis for historical biogeography. [Link to sourceforge]
Text
Nylander, J.A.A., C. Erséus, and M. Källersjö. 1999. A test of monophyly of the gutless Phallodrilinae (Oligochaeta, Tubificidae) and the use of a 573 bp region of the mitochondrial cytochrome oxidase I gene in analysis of annelid phylogeny. Zoologica Scripta 28:305-313. [PDF/BIB]
Nylander, J.A.A. 2001. Taxonomic sampling in phylogenetic analysis: Problems and strategies reviewed. Introductory Research Essay No. 1. Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University. [PDF/BIB]
Rokas, A., J.A.A. Nylander, F. Ronquist and G.N. Stone. 2002. A maximum likelihood analysis of eight phylogenetic markers in gallwasps (Hymenoptera: Cynipidae); implications for insect phylogenetic studies. Molecular Phylogenetics and Evolution 22:206-219. [PDF/BIB]
Nylander, J.A.A., F. Ronquist, J.P. Huelsenbeck, and J.L. Nieves Aldrey. 2004. Bayesian phylogenetic analysis of combined data. Systematic Biology 53:47-67. [PDF/BIB]
Nylander, J.A.A. 2004. Bayesian phylogenetics and the evolution of gall wasps. Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1104-232X ;937. [PDF/BIB]
Irestedt, M, J. Fjeldså, J.A.A. Nylander, and P.G.P. Ericson. 2004. Phylogenetic relationships of typical Antbirds (Thamnophilidae) and test of incongruence based on Bayes factors. BMC Evolutionary Biology 4:23. [PDF/BIB]
Beier, B.-A., J.A.A. Nylander, M.W. Chase, and M. Thulin. 2004. Phylogenetic relationships and biography of the desert plant genus Fagonia (Zygophyllaceae), inferred by parsimony and Bayesian model averaging. Molecular Phylogenetics and Evolution 33:91-108. [PDF/BIB]
Buffington, M.L., J.A.A. Nylander, and J.M. Heraty. 2007. The phylogeny and evolution of Figitidae (Hymenoptera: Cynipoidea). Cladistics 23:403-431. [PDF/BIB]
Nylander, J.A.A., J.C. Wilgenbush, D.L. Warren, and D.L. Swofford. 2008. AWTY (Are We There Yet?): A system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24:581-583. [PDF/BIB]
Nylander, J.A.A., U. Olsson, P. Alström, and I. Sanmartín. 2008. Accounting for phylogenetic uncertainty in biogeography: A Bayesian approach to dispersal- vicariance analysis of the thrushes (Aves: Turdus). Systematic Biology 57:257-268. [PDF/BIB]
Buerki, S., F. Forest, P. Acevedo-Rodríguez, M.W. Callmander, J.A.A. Nylander, M. Harrington, I. Sanmartín, P. Küpfer, and N. Alvarez. 2009. Plastid and nuclear DNA markers reveal intricate relationships at subfamilial and tribal levels in the soapberry family (Sapindaceae). Molecular Phylogenetics and Evolution 51:238-258. [PDF/BIB]
Lundberg, M., M. Töpel, B. Eriksen, J.A.A. Nylander, and T. Eriksson. 2009. Allopolyploidy in Fragariinae (Rosaceae): Comparing four DNA sequence regions, with comments on classification. Molecular Phylogenetics and Evolution 51:269-280. [PDF/BIB]
Antonelli, A., J.A.A. Nylander, C. Persson, and I. Sanmartín. 2009. Tracing the impact of the Andean uplift on Neotropical plant evolution: evidence from the coffee family. Proceedings of the National Academy of Sciences 106:9749-9754. [PDF/BIB]
Nieves-Aldrey, J.L., J. Liljeblad, M. Hernández Nieves, A. Grez, and J.A.A. Nylander. 2009. Revision and phylogenetics of the genus Paraulax Kieffer (Hymenoptera, Cynipidae) with biological notes and description of a new tribe, a new genus, and five new species . Zootaxa 2200:1-40. [PDF/BIB]
Buckley, T.R., D. Attanayake, J.A.A. Nylander, and S. Bradler. 2009. The phylogenetic placement and biogeographical origins of the New Zealand stick insects (Phasmatodea). Systematic Entomolgy 35:205-225. [PDF/BIB]
Ran, L., J. Larsson, T. Vigil-Stenman, J.A.A. Nylander, K. Ininbergs, W.-W. Zheng, A. Lapidus, S. Lowry, R. Haselkorn and B. Bergman. 2010. Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium. PLoS ONE NN:NNN. [PDF/BIB]
Buerki, S., F. Forest, N. Alvarez, J.A.A. Nylander, N. Arrigo, and I. Sanmartín. In press. An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the worldwide plant soapberry family (Sapindaceae). In press. Journal of Biogeography NN:NNN--NNN. [PDF/BIB]
Jønsson, K.A., R.C.K. Bowie, J.A.A. Nylander, L. Christidis, J.A. Norman, and J. Fjeldså. In press. Biogeographical history of cuckoo-shrikes (Aves: Passeriformes): transoceanic colonization of Africa from Australo-Papua. Journal of Biogeography NN:NNN--NNN. [PDF/BIB]
Lists
X Birds and vipers seen in nature (in Swedish).
Links
