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angsd

Program for analysing NGS data.

bam2iupac

IUPAC FASTA extraction from BAM files to stdout

bio-scripts

collection of scripts for bioinformatic analysis

bioconda-recipes

Conda recipes for the bioconda channel.

breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R. More information at

colabfold

Making Protein folding accessible to all!

crbhits

[CRBHits](https://github.com/kullrich/CRBHits) is a reimplementation of the Conditional Reciprocal Best Hit algorithm [crb-blast](https://github.com/cboursnell/crb-blast) in R.

dagchainer

Fork of the DAGchainer project https://sourceforge.net/projects/dagchainer

dist2bionjs

Use stdin distance matrix to calculate bionjs

diststring

distSTRING calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

eurobioc2022_msa2dist

Slide presentation and material for the software demo "Downstream Analysis of Synteny Networks with MSA2dist"

funbiased

genes2functions

This is a shiny app built around clusterProfiler to perform functional enrichment analysis from RNA-Seq DE analysis

genome-grid

genomeannotator

Pipeline for the identification of (coding) gene structures in draft genomes.

introgression

jstacs

kakscalculator2

Fork of the KaKs_Calculator2.0 project https://sourceforge.net/projects/kakscalculator2

kortho

kortho calculates pairwise kmer jaccard distance between two peptide fasta files

korthocpp

korthoCPP calculates pairwise kmer jaccard distance between two peptide fasta files

korthor

korthoR calculates pairwise kmer jaccard distance between all sequences of an AAStringSet

kullrich.github.io

Personal website

literal-dists

Convert a FASTA alignment with ambiguous nucleotides to literal distance matrix

lordec-miniasm

ltc_palettes

minipileup

Simple pileup-based variant caller

msa2dist

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

mytai

Evolutionary Transcriptomics with R

oggmap

oggmap is a python package to extract orthologous maps (short: orthomap or in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Oggmap results (gene ages per orthologous group) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

orthofinder

Phylogenetic orthology inference for comparative genomics