kullrich

snpless-nf

snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.

bio-scripts

collection of scripts for bioinformatic analysis

kakscalculator2

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

orthomap

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

MSA2dist

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

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.

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.

scTEI

add any phylogenetically based transcriptome evolutionary index (TEI) to single-cell data objects

EuroBioc2022_MSA2dist

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

korthoR

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

angsd

Program for analysing NGS data.

bioconda-recipes

Conda recipes for the bioconda channel.

ColabFold

Making Protein folding accessible to all!

genome-grid

genomeannotator

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

introgression

Jstacs

kortho

kortho calculates pairwise kmer jaccard distance between two peptide fasta files

korthoCPP

korthoCPP calculates pairwise kmer jaccard distance between two peptide fasta files

literal-dists

Convert a FASTA alignment with ambiguous nucleotides to literal distance matrix

lordec-miniasm

minipileup

Simple pileup-based variant caller

OrthoFinder

Phylogenetic orthology inference for comparative genomics

orthohmmer

Orthology inference based on hmmer

published_phylomaps

A Collection of Published Phylostratigraphic Maps and Divergence Maps

SAMap

SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.

syntenet

An R package to infer and analyze synteny networks from protein sequences

syntenyPlotteR

R package to draw syntenic plots in 3 different styles

tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission

TreeSwitchR

TreeSwitchR visualize phylogenetic trees along chromosomes in R