54 Open source projects that are alternatives of or similar to r2g

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

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

Bioinformatics curated workflows that use Biocontainers tools

Distribution of TEs and their relationship to genes in host genome

Improve the quality of a denovo assembly by scaffolding and gap filling

Ultrafast Sample Placement on Existing Trees

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Sequential Tree Sampler for online phylogenetics

♥ Fast and Accurate Estimation of Evolutionary Distances

Finds SNP sites from a multi-FASTA alignment file

A Python package for gene-centric taxonomic and functional classification using phylogenetic placement

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

<<------ Use SnapATAC!!

A tool for exploring very large trees in the browser

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

Distances and representations of persistence diagrams

Real-time species-typing visualisation for nanopore data.

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

Build and maintain multiple custom conda environments all in once place.

Predict plasmids from uncorrected long read data

Sentieon DNAseq

Assembling the cause of phenotypes and genotypes from NGS data

Bystro genetic analysis (annotation, filtering, statistics)

Ploidy agnostic phasing pipeline and algorithm

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

A modular annotation tool for genomic variants

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

Python toolkit for building restartable pipelines

Multilocus sequence typing by blast using the schemes from PubMLST

GREIN : GEO RNA-seq Experiments Interactive Navigator

A bioinformatics pipeline to analyze mtDNA from NGS data

Official git repository for Biopython (originally converted from CVS)

Phylogenetic Likelihood Library

Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.

Phylogenetic trees in Julia

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

Version 5 of the CAFE phylogenetics software

A library for working with phylogenetic and population genetic data.

Python version of PHLAWD

A course in the theory and practice of phylogenetic inference from DNA sequence data

PhyML -- Phylogenetic estimation using (Maximum) Likelihood

Alignment editor for Mac OS X

Ancestor character reconstruction and visualisation for rooted phylogenetic trees

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

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

baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

Implementing semantically rich NeXML I/O in R

Biological Sequence Substitution Models for Julia

booster.c3bi.pasteur.fr

R pipeline for computing persistent homology in topological data analysis. See https://doi.org/10.21105/joss.00860 for more details.