Projects in Awesome Lists by nylander
A curated list of projects in awesome lists by nylander .
https://github.com/nylander/catfasta2phyml
Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file
Last synced: 22 Jul 2025
https://github.com/nylander/mrmodeltest2
C program for selecting DNA substitution models using PAUP*
Last synced: 05 Mar 2025
https://github.com/nylander/burntrees
Perl scripts for manipulating output from phylogenetic MCMC software (MrBayes, BEAST, PhyloBayes, etc)
Last synced: 05 Mar 2025
https://github.com/nylander/get_fasta_info
Some useful summary tools for FASTA formatted files
Last synced: 09 Mar 2026
https://github.com/nylander/beast2phy
Convert output trees from BEAST to other formats
Last synced: 06 Feb 2026
https://github.com/nylander/translate_fasta_headers
Translate long fasta headers to short - and back!
Last synced: 05 Mar 2025
https://github.com/nylander/fastagap
Remove or replace gaps in fasta formatted files
Last synced: 05 Mar 2025
https://github.com/nylander/grepfasta
Yet another grep for FASTA formatted files - with regexp capacity!
Last synced: 05 Mar 2025
https://github.com/nylander/check_md5sums
Check md5 sums for all .md5 and MD5SUMS files found in directory tree
Last synced: 05 Mar 2025
https://github.com/nylander/plotmcmcoutput
Shell scripts (bash) for plotting MCMC output (e.g., from MrBayes v.3, BEAST, etc) using gnuplot
Last synced: 06 Mar 2026
https://github.com/nylander/phy2fas
Phylip to fasta converter using BioPerl
Last synced: 19 Apr 2026
https://github.com/nylander/diva-dispersal-vicariance-analysis
Downloaded from SourceForge
Last synced: 26 May 2026
https://github.com/nylander/run-mrbayes-on-uppmax
Notes on running MrBayes on UPPMAX compute resources
Last synced: 05 Mar 2025
https://github.com/nylander/saturation.plot
Code for for displaying the relationship between the uncorrected (P-) distance and the distance on a phylogenetic tree
Last synced: 05 Mar 2025
https://github.com/nylander/align-and-trees-parallel-workflow
Script for running a "standard" phylogenetic workflow on fasta-formatted input. In particular, parallel execution is done whenever possible.
Last synced: 20 Jul 2025
https://github.com/nylander/easy_webshare_on_uppmax
Easy file sharing on UPPMAX
Last synced: 05 Mar 2025
https://github.com/nylander/mraic
Perl script for selecting DNA substitution models using PhyML
Last synced: 14 Oct 2025
https://github.com/nylander/fastear
FastEAR - Fast(er) Extraction of Alignment Regions from FASTA
Last synced: 05 Mar 2025
https://github.com/nylander/taxid2scientific_name
Get scientific name from Genbank taxon ID - or the other way around
Last synced: 16 Apr 2026
https://github.com/nylander/efasta2fasta
Convert extended fasta (efasta) to fasta
Last synced: 27 Jun 2025
https://github.com/nylander/reformatkml
Reformat KML files. Script used in Stephan Nylinder et al. "On the Biogeography of Centipeda: A Species Tree Diffusion Approach". Syst. Biol.
Last synced: 13 Oct 2025
https://github.com/nylander/norm-file-format
Convert any document to .norm format
Last synced: 01 Jun 2026
https://github.com/nylander/plot-yangs-gamma
Plot the Gamma distribution used by Ziheng Yang (1996)
Last synced: 19 Apr 2026
https://github.com/nylander/parse_mrbayes_ancestral_states
Create FASTA file for ancestral sequence reported in MrBayes v.3
Last synced: 19 Apr 2026
https://github.com/nylander/bp2mb
Convert trees from Pagel's BayesPhylogenies to MrBayes format
Last synced: 21 Apr 2026
https://github.com/nylander/mailfit
Perl script that runs PAUP and MrModeltest2 (or Modeltest) and sends (optionally) results via e-mail.
Last synced: 09 May 2026
https://github.com/nylander/neworder
Permute the order of ordered character states
Last synced: 10 May 2026
https://github.com/nylander/split-fasta-seq
Split long fasta entries to shorter - and fast!
Last synced: 10 May 2026
https://github.com/nylander/bbb
Class-room Linux Server on the BeagleBone Black
Last synced: 10 May 2026
https://github.com/nylander/md2pdf
Markdown to plain PDF or Beamer-slides. Examples.
Last synced: 22 Apr 2026
https://github.com/nylander/likelihood-mapping-with-iqtree
Likelihood-mapping in iqtree2
Last synced: 26 Jun 2025
https://github.com/nylander/exercise_for_working_with_stderr_and_stdin
Simple exercise for working with STDERR, STDIN, and transferring files from and to a server
Last synced: 12 May 2026
https://github.com/nylander/plotsimmap
R script for plotting output from SIMMAP's ancestral state reconstructions
Last synced: 05 Mar 2025
https://github.com/nylander/run-bayes-diva
Some scripts used for the "Bayes-DIVA" analysis of Thrushes in Nylander et al. 2008.
Last synced: 05 Jul 2025
https://github.com/nylander/fasta2mlcalc
Create a distance matrix for Paul Lewis's MLCalc program from a fasta-formatted sequence file
Last synced: 05 Mar 2025
https://github.com/nylander/454_tag_sorting
Script for finding paired tags ("Binladen tags") in 454 data
Last synced: 05 Mar 2025
https://github.com/nylander/compare_two_files
Compare the content of two files (line by line)
Last synced: 05 Mar 2025
https://github.com/nylander/myman
Find and display files in your myman folder using TAB completion
Last synced: 21 Apr 2026
https://github.com/nylander/degap_fasta_alignment
Remove columns in large fasta formatted alignments containing all-missing data.
Last synced: 28 Jul 2025
https://github.com/nylander/mlst-blast
Scripts for conducting multi-locus sequencing typing against the pubmlst.org database using blast.
Last synced: 02 Aug 2025
https://github.com/nylander/remove_mcmc_output
Remove all those files generated by phylogenetic MCMC software
Last synced: 27 May 2026
https://github.com/nylander/modelfit
Perl wrappers to Modeltest and MrModeltest
Last synced: 18 Apr 2026
https://github.com/nylander/awesome
My settings for the tiling windows manager "awesome"
Last synced: 29 May 2026
https://github.com/nylander/resample_fasta
Resample large FASTA alignments - fast!
Last synced: 05 Oct 2025