Latest update: Dec 19 2011
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]
pMrAIC
v.
1.1. This version of MrAIC runs parallel instances of PHYML, and has functionality for submitting PHYML runs to clusters.
README.
MrModeltest2
v.
2.3. C program for selecting DNA substitution models using PAUP*.
README
[WIN/MACOSX/UNIX] 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).
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