nylander
Bioinformatician at Naturhistoriska riksmuseet (NRM). Affiliated with Stockholm University.
@Naturhistoriska, @NBISwedenSweden
Pinned Repositories
beast2phy
Convert output trees from BEAST to other formats
Burntrees
Perl scripts for manipulating output from phylogenetic MCMC software (MrBayes, BEAST, PhyloBayes, etc)
catfasta2phyml
Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file
Check_MD5SUMS
Check md5 sums for all .md5 and MD5SUMS files found in directory tree
fastagap
Remove or replace gaps in fasta formatted files
get_fasta_info
Some useful summary tools for FASTA formatted files
grepfasta
Yet another grep for FASTA formatted files - with regexp capacity!
MrModeltest2
C program for selecting DNA substitution models using PAUP*
plotMCMCoutput
Shell scripts (bash) for plotting MCMC output (e.g., from MrBayes v.3, BEAST, etc) using gnuplot
translate_fasta_headers
Translate long fasta headers to short - and back!
nylander's Repositories
nylander/beast2phy
Convert output trees from BEAST to other formats
nylander/Check_MD5SUMS
Check md5 sums for all .md5 and MD5SUMS files found in directory tree
nylander/DIVA-Dispersal-Vicariance-Analysis
Downloaded from SourceForge
nylander/efasta2fasta
Convert extended fasta (efasta) to fasta
nylander/OrthoFinder
Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy". **The diamond branch have support for using DIAMOND instead of BLAST+.**
nylander/pMrAIC
Parallel MrAIC
nylander/prequal
PREQUAL: a pre-alignment quality filter for comparative sequence analyses
nylander/454_tag_sorting
Script for finding paired tags ("Binladen tags") in 454 data
nylander/BBB
Class-room Linux Server on the BeagleBone Black
nylander/bp2mb
Convert trees from Pagel's BayesPhylogenies to MrBayes format
nylander/Mailfit
Perl script that runs PAUP and MrModeltest2 (or Modeltest) and sends (optionally) results via e-mail.
nylander/MrBayes-exercise
Simple MrBayes exercise
nylander/nexus.vim
Syntax highlighting for Nexus file format
nylander/phytools
nylander/PlotSimMap
R script for plotting output from SIMMAP's ancestral state reconstructions
nylander/Resample_fasta
Resample large FASTA alignments - fast!
nylander/run-Bayes-DIVA
Some scripts used for the "Bayes-DIVA" analysis of Thrushes in Nylander et al. 2008.