MethPhaser: methylation-based haplotype phasing of human genomes

GEMsembler tool for assembling and comparing several types of Genome-Scale Metabolic Models (GEMs)

🚀 seqfu - Sequece Fastx Utilities

Dissecting data structures

Software suite for the automated generation of geographically correct or schematic transit maps.

TEtrimmer: a novel tool to automate manual curation of transposable elements

A small-RNA sequencing analysis pipeline

Python package to study microbial communities using metabolic modeling.

A C++ drop-in replacement of FastQC to assess the quality of sequence read data

CarveMe: genome-scale metabolic model reconstruction

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Extensive de-novo TE Annotator

A modern and intuitive terminal-based text editor

LexicMap: efficient sequence alignment against millions of prokaryotic genomes

A django/python frontend that uses NCBIs standalone blast to identify Insertion Sequences in genbank files

A versatile cutting tool for R

A modern alternative to ls

IQ-TREE version 3: software for phylogenetics

Three level Amalgamated Likelihood Estimation (TALE): 3-Level reconciliation of host/symbiont/gene trees, and python reimplementation of ALE, 2-level gene/species reconciliation.

Simple and Customizable Tables in `R`

general purpose library for evaluating the likelihood of sequence evolution on trees

Bayesian analysis of genomic sequence data under the multispecies coalescent model

repositioning and resizing of images directly in quarto revealjs slides

Find endogenous viral elements in genomes

Reorients assembled microbial sequences

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!