nylander

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/catfasta2phyml

Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file

nylander/translate_fasta_headers

Translate long fasta headers to short - and back!

nylander/fastagap

Remove or replace gaps in fasta formatted files

nylander/grepfasta

Yet another grep for FASTA formatted files - with regexp capacity!

nylander/plotMCMCoutput

Shell scripts (bash) for plotting MCMC output (e.g., from MrBayes v.3, BEAST, etc) using gnuplot

nylander/reorient_fasta

Reverse-complement DNA sequences as needed in relation to a reference. Based on blastn.

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.

nylander/bioconda-recipes

Conda recipes for the bioconda channel.

nylander/consensus-sequence

nylander/FastEAR

FastEAR - Fast(er) Extraction of Alignment Regions from FASTA

nylander/fastp-cleaning

Clean fastq files with fastp

nylander/ptemplate

ptemplate -- A project template

nylander/saturation.plot

Code for for displaying the relationship between the uncorrected (P-) distance and the distance on a phylogenetic tree

nylander/taxid2scientific_name

Get scientific name from Genbank taxon ID - or the other way around

nylander/abc.se

My abc.se web page

nylander/awesome

My settings for the tiling windows manager "awesome"

nylander/birdscanner2

nylander/dds_cli

The command line interface for access to the Data Delivery System primarily developed by the SciLifeLab Data Centre.

nylander/Exercise_for_working_with_STDERR_and_STDIN

Simple exercise for working with STDERR, STDIN, and transferring files from and to a server

nylander/HMMer-parser

nylander/leeHom

Bayesian reconstruction of ancient DNA fragments

nylander/likelihood-mapping-with-iqtree

Likelihood-mapping in iqtree2

nylander/MACSE_V2_PIPELINES

This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MACSE. These pipelines are mostly bash scripts encapsulated within singularity containers and sometimes combined in nextflow workflows.

nylander/neworder

Permute the order of ordered character states

nylander/nf-GL_popstructure

Nextflow pipeline that calculates genotype likelihoods in angsd from a list of bamfiles and plots admixture trhough NGSadmix and PCAs through PCAngsd.

nylander/nylander.github.io

Web page for Johan Nylander

nylander/ParGenes

A massively parallel tool for model selection and tree inference on thousands of genes

nylander/vim

My setup for vim

nylander/vim-template

Simple templates plugin for Vim

nylander/xlsx2tsv

A simple utility to dump the first sheet of a .xlsx file to stdout in TSV format