40 Open source projects that are alternatives of or similar to RDPTools

Compare different differential abundance and expression methods

Various functions for analysis of microbial community data

Rust implementation of sequence alignment / Levenshtein distance by A* acceleration of the DP algorithm

Collection of scripts for bacterial genomics

A fast multiple sequence alignment program.

BISulfite-seq CUI Toolkit

scripts and notes for learning

A fast and scalable phylogenetic tree viewer for microbiome data analysis

A model-based visualization method for microbiome data

MaAsLin2: Microbiome Multivariate Association with Linear Models

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Rapid determination of appropriate reference genomes.

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

A MALDI Mass Spectrometry Bioinformatics Platform

Metagenomic pipeline and other general scripts used in the lab.

Sample search by metadata and features

The Microbiome Interpretable Temporal Rule Engine

Schloss Lab Tools for Reproducible Microbiome Research 💩

R package for microbiome biomarker discovery

Qiita - A multi-omics databasing effort

exploratory and interactive microbiome analyses based on heatmaps

Visualize microbiome data with black magic ggtree

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples

ganon classifies short DNA sequences against large sets of genomic sequences efficiently, with download and update of references (RefSeq/Genbank), taxonomic (NCBI/GTDB) and hierarchical classification, customized reporting and more

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

Cross-disease comparison of case-control gut microbiome studies

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

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

Implementation of Machine Learning Algorithms

Official git repository for Biopython (originally converted from CVS)

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

DOM Text Based Multiple Sequence Alignment Library

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Collection of sequence alignment algorithms.

Neural Networks for Protein Sequence Alignment

Sequence alignment tools

The Modular Aligner and The Modular SV Caller

SneakySnake🐍 is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.org/abs…