Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.

Finds SNP sites from a multi-FASTA alignment file

Scripts and data files relevant to the manuscript: "Evidence for a multi-level trophic organization of the human gut microbiome"

Prodigal Gene Prediction Software

A Grammar of Graphics for Python

A platform for transforming command-line applications into a job service.

🌌 The R easystats-project

🔗 Methods for Correlation Analysis

sc-im - Spreadsheet Calculator Improvised -- An ncurses spreadsheet program for terminal

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Proteins as words, genomes as documents.

SMETANA: a tool to analyse interactions in microbial communities

CarveMe: genome-scale metabolic model reconstruction

Estimated marginal means

A burrows-wheeler transform-based probabilistic short read mapper.

Metagenomics-related extended functionalities to samtools

👻 Utilities for analyzing Bayesian models and posterior distributions

Virus Identification By iteRative ANnoTation

De novo Extraction of Strains from MetAgeNomes

Variational autoencoder for metagenomic binning

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

Using the jedi autocompletion library for VIM.

R package for fast & exact (restricted) likelihood ratio tests for mixed and additive models

MMseqs2: ultra fast and sensitive search and clustering suite

A game theoretic approach to explain the output of any machine learning model.

Scripts to download genomes from the NCBI FTP servers

A fast whole-genome aligner based on de Bruijn graphs

glmmTMB