Burntrees v. 0.1.9. 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.

Beast2Phy. Perl and shell (bash) scripts for converting BEAST/TreeAnnotator output to a format readable by other software. README.

catfasta2phyml.pl. Perl script for concatenating alignments in FASTA format to Phyml/Phylip format. README.

gnuplot MCMC output. Shell (bash) scripts for plotting MCMC output (e.g. from MrBayes, BEAST, etc) using gnuplot. 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/Suppl./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 5(7):e11486. [PDF/Suppl./BIB]

Jønsson, K.A., R.C.K. Bowie, J.A.A. Nylander, L. Christidis, J.A. Norman, and J. Fjeldså. 2010. Biogeographical history of cuckoo-shrikes (Aves: Passeriformes): transoceanic colonization of Africa from Australo-Papua. Journal of Biogeography 37:1767-1781. [PDF/BIB]

Buerki, S., F. Forest, N. Alvarez, J.A.A. Nylander, N. Arrigo, and I. Sanmartín. 2011. An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the worldwide plant soapberry family (Sapindaceae). Journal of Biogeography 38:531-550. [PDF/BIB]

Larsson, J., J.A.A. Nylander, and B. Bergman. 2011. Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits. BMC Evolutionary Biology 11:187. [PDF/Suppl./BIB]

Lists

X Birds and vipers seen in nature (in Swedish).

Links