nylander/plotMCMCoutput
Shell scripts (bash) for plotting MCMC output (e.g., from MrBayes v.3, BEAST, etc) using gnuplot
Developer Profile
nylander
Discovered public repositories for nylander in the GitHub catalog.
nylander/reformatKML
Reformat KML files. Script used in Stephan Nylinder et al. "On the Biogeography of Centipeda: A Species Tree Diffusion Approach". Syst. Biol.
nylander/remove_mcmc_output
Remove all those files generated by phylogenetic MCMC software
nylander/translate_fasta_headers
Translate long fasta headers to short - and back!
nylander/run-Bayes-DIVA
Some scripts used for the "Bayes-DIVA" analysis of Thrushes in Nylander et al. 2008.
nylander/MrModeltest2
C program for selecting DNA substitution models using PAUP*
nylander/MrAIC
Perl script for selecting DNA substitution models using PhyML
nylander/Fasta2MLCalc
Create a distance matrix for Paul Lewis's MLCalc program from a fasta-formatted sequence file
nylander/beast2phy
Convert output trees from BEAST to other formats
nylander/Modelfit
Perl wrappers to Modeltest and MrModeltest
nylander/Mailfit
Perl script that runs PAUP and MrModeltest2 (or Modeltest) and sends (optionally) results via e-mail.
nylander/compare_two_files
Compare the content of two files (line by line)
nylander/bp2mb
Convert trees from Pagel's BayesPhylogenies to MrBayes format
nylander/catfasta2phyml
Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file
nylander/get_fasta_info
Some useful summary tools for FASTA formatted files
nylander/grepfasta
Yet another grep for FASTA formatted files - with regexp capacity!
nylander/PlotSimMap
R script for plotting output from SIMMAP's ancestral state reconstructions
nylander/Burntrees
Perl scripts for manipulating output from phylogenetic MCMC software (MrBayes, BEAST, PhyloBayes, etc)
nylander/pMrAIC
Parallel MrAIC