lczech

Postdoc in bioinformatics :seedling: and computer scientist :octocat: working on inter-disciplinary ways to save the planet :earth_africa:

Globe Institute, Section for GeoGenetics University of Copenhagen, Denmark

Pinned Repositories

gappa
A toolkit for analyzing and visualizing phylogenetic (placement) data
Language:C++57 7 287
genesis
A library for working with phylogenetic and population genetic data.
Language:C++56 9 512
grenedalf
Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments
Language:C++25 3 202
HAF-pipe
Calculate haplotype-derived allele frequencies for pool-seq samples
Language:Shell1 1 00
nidhoggr
Snakemake pipeline to run phylogenetic tree inferences
Language:Python4 4 01
popoolation2
Forked from https://sourceforge.net/p/popoolation2/
Language:Perl2 3 00
thesis
My dissertation / PhD thesis
Language:TeX4 5 00
grenepipe
A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.
Language:Python79 4 4718
HAFpipe-line
calculate haplotype-derived allele frequencies for pool-seq samples
Language:Shell6 9 81
swarm
A robust and fast clustering method for amplicon-based studies
Language:C++120 13 17723

lczech's Repositories

lczech/gappa
A toolkit for analyzing and visualizing phylogenetic (placement) data
Language:C++57 7 287
lczech/genesis
A library for working with phylogenetic and population genetic data.
Language:C++56 9 512
lczech/grenedalf
Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments
Language:C++25 3 202
lczech/nidhoggr
Snakemake pipeline to run phylogenetic tree inferences
Language:Python4 4 01
lczech/thesis
My dissertation / PhD thesis
Language:TeX4 5 00
lczech/popoolation2
Forked from https://sourceforge.net/p/popoolation2/
Language:Perl2 3 00
lczech/HAF-pipe
Calculate haplotype-derived allele frequencies for pool-seq samples
Language:Shell1 1 00
lczech/placement-methods-paper
Accompanying code repository with scripts, programs and data for our papers.
Language:C++11
lczech/pool-seq-pop-gen-stats
Language:TeX1 4 00
lczech/CLI11
Command line parser for C++11
Language:C++3 0
lczech/come_2017
Some sample files for the CoME2017 course to play around with.
Language:C++3 1
lczech/dinoflagellate-paper
Code repository for the dinophyte DNA in tropical rain forest soils paper
Language:Shell3 0
lczech/eseb-birds
Language:HTML3 01
lczech/flat
Flat containers for C++
Language:C++3 0
lczech/genesis-gappa-paper
Scripts and Tests for the Application Note of genesis and gappa
Language:Shell4 0
lczech/grenedalf-paper
Code for tests and benchmarks of our paper on grenedalf
Language:Python3 0
lczech/grenepilot-paper
Scripts and analyses for the GrENE-net pilot dataset
Language:R5 0
lczech/greneselect
Snakemake playground for selection analyses in evolve & resequence experiments
Language:Python3 0
lczech/htscodecs
Custom compression for CRAM and others.
Language:C1 0
lczech/language-cpp
C++ support in Atom
Language:CoffeeScript3 0
lczech/lucas-dark-syntax
My syntax scheme for atom.
Language:CSS3 0
lczech/papara_nt
new codebase of the PaPaRa algorithm
Language:C++4 0
lczech/pllprac
Programming Practical of the Exelicis Lab using the Phylogenetic Likelihood Library
Language:C++
lczech/PoolHMM
Pool-HMM mirror with Mac support (versions >= 1.4.3)
Language:Python
lczech/popoolation
Forked from https://sourceforge.net/p/popoolation/
Language:Perl3 0
lczech/ratatosk
Snakemake pipeline for phylogenetic placement of metagenomic sequences
Language:Python4 0
lczech/snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
lczech/sparsepp
A fast, memory efficient hash map for C++
lczech/swarm
A robust and fast clustering method for amplicon-based studies
Language:C++3 0
lczech/zstr
A C++ header-only ZLib wrapper
Language:C++2 0