This repository contains Dockerfiles used to build Docker images for bioinformatics tools, with a focus on evolutionary biology and phylogenetics. All images are published on DockerHub under the evolbioinfo organization.
A tentative of matching between the containerized tools and bio.tools is described in BIOTOOLS.md .
Each image is hosted on DockerHub under evolbioinfo/<tool-name>:<version>. To pull an image:
docker pull evolbioinfo/< tool-name> :< version> For example, to pull the RAxML-NG image:
docker pull evolbioinfo/raxml-ng:v1.2.2 Most images define an ENTRYPOINT pointing directly to the tool executable. You can run a tool as follows:
docker run evolbioinfo/< tool-name> :< version> [tool options] For example, to display the RAxML-NG help:
docker run evolbioinfo/raxml-ng:v1.2.2 --help Or to run FastTree:
docker run evolbioinfo/fasttree:v2.2.0 -help To use your local files inside the container, mount your working directory using the -v flag:
docker run -v /path/to/your/data:/data evolbioinfo/< tool-name> :< version> [tool options] For example, to run RAxML-NG on a local alignment file:
docker run -v $( pwd) The versions listed represent the latest containerized builds in this repository, not necessarily the most recent versions of the underlying tools.
Tool Latest Version Description Bio++ v3.0.0 The Bio++ Libraries for phylogenetic and sequence analysis ebg v0.13.3 Educated Bootstrap Guesser epa-ng v0.3.8 Evolutionary placement algorithm for short reads into reference trees fastme v2.1.6.4 Fast and accurate distance-based phylogenetic tree construction fasttree v2.2.0 Approximate maximum-likelihood phylogenetic trees for large alignments goalign v0.4.0 Multiple sequence alignment analysis toolkit gotree v0.5.1 Phylogenetic tree manipulation toolkit guppy v3.1.5 Tools for working with pplacer phylogenetic placement files iqtree v3.1.1 Fast and accurate maximum-likelihood phylogenetic tree inference lsd v0.3.3 Least-squares dating of phylogenetic trees lsd2 v2.4.1 Least-squares dating of phylogenetic trees (version 2) maple v0.7.5 Maximum likelihood phylogenetic estimation with reduced memory ml_bootstrap fec985c Machine learning based support (see this article ) mrbayes v3.2.7 Bayesian inference of phylogenetic trees newick_utilities v1.6 Utilities for manipulating Newick format trees ngphylogeny_multitools seqtype_detect Multi-tool image for phylogenetic workflows phylodeep v0.9 Deep learning for phylodynamic parameter estimation phyml v3.3.20260528 Maximum-likelihood phylogenetic tree estimation phyml-sms v1.8.1.1 PhyML with Smart Model Selection ptp v4bb2daf Species delimitation from phylogenetic trees rappas v1.21 Rapid alignment-free phylogenetic identification via statistical hypothesis testing raxml v8.2.13 Randomized accelerated maximum likelihood phylogenetic inference raxml-ng v2.0.2 RAxML next-generation RogueNaRok v1.0.1 Algorithm for the identification of rogue taxa in a tree set table2itol latest Converts annotation tables to iTOL dataset files tqdist v1.0.2 Computing quartet and triplet distances between trees treedater 89a0df0 Scalable relaxed clock phylogenetic dating treemmer v0.3 Reduce tree size while preserving phylogenetic diversity treesimulator v0.2.27 Simulating rooted phylogenetic trees under various models treestructure a831a66 Identification of hidden population structure in time-scaled phylogenies treetime v0.11.4 Maximum-likelihood phylogenetic time-trees inference treewas v1.1 Genome-wide association studies on phylogenetic trees
Tool Latest Version Description bmge v2.00 Block Mapping and Gathering with Entropy for alignment trimming clustal_omega v1.2.4 Fast and scalable multiple sequence alignment gblocks v1.0 Alignment trimming by selecting conserved blocks lastal v980 Local alignment of biological sequences mafft v7.526 Multiple sequence alignment using fast Fourier transform muscle v5.3 Multiple sequence alignment noisy v1.5.12 Identify homoplastic characters in multiple sequence alignments tcoffee Version_13.46.2.7c9e712d Multiple sequence alignment using T-Coffee trimal v1.5.1 Automated removal of spurious sequences or poorly aligned regions
Tool Latest Version Description bbmap v39.81 Short read aligner for DNA and RNA-seq data bowtie v1.3.1 Aligning sequencing reads to references bowtie2 v2.5.5 Mapping DNA sequences against a large reference genome bwa v0.7.19 Burrows-Wheeler aligner for short DNA sequences bwa-mem2 v2.2.1 The next version of bwa-mem hisat2 v2.2.2 Alignment program for mapping next-generation sequencing reads to a population of human genomes mash v2.3 Fast genome and metagenome distance estimation using MinHash minimap2 v2.30 Versatile pairwise aligner for genomic and spliced nucleotide sequences papara v2.5 Phylogeny-aware short-read alignment star v2.7.11b Spliced Transcripts Alignment to a Reference (RNA-seq)
Tool Latest Version Description alfred v0.5.3 BAM alignment statistics, feature counting and feature annotation bam-readcount v1.0.1 Per-position read counts from BAM files bamUtil v1.0.15 Programs for working on SAM/BAM files bedtools v2.31.1 Genome arithmetic and interval manipulation dsrc v2.0.2 DNA sequence compression tool fastqutils v0.1.7 Utilities for manipulating FASTQ files fastxtoolkit v0.0.14 FASTX toolkit for preprocessing FASTQ/FASTA files gofasta v1.2.3 Command-line utilities for working with genomic alignments picard v3.4.0 Command-line tools for manipulating high-throughput sequencing data samtools v1.23.1 Reading, writing, and manipulating SAM/BAM/CRAM files seqkit v2.13.0 Ultrafast toolkit for FASTA/Q file manipulation seqtk v1.5 Toolkit for processing sequences in FASTA/Q formats sra-tools v3.0.1 NCBI SRA toolkit for downloading and processing sequencing data sratoolkit v3.0.1 Alternate NCBI SRA toolkit image vcftools v0.1.17 Tools for working with VCF files
Tool Latest Version Description bcftools v1.23.1 VCF/BCF variant manipulation and calling freebayes v1.3.10 Bayesian genetic variant detector ivar v1.4.4 Tools for viral amplicon-based sequencing
Tool Latest Version Description catch v1.5.2 Compact Aggregation of Targets for Comprehensive Hybridization fastqc v0.12.1 Quality control analysis of high-throughput sequencing data minionqc v1.4.2 Quality control for Oxford Nanopore sequencing data multiqc v1.9 Aggregate bioinformatics results across samples into a report nanoplot v1.47.1 Plotting tools for long-read sequencing data rna-seqc v1.1.9 Quality control metrics for RNA-seq data
Tool Latest Version Description adapterremoval v2.3.3 Trimming of adapters and low-quality bases from NGS reads alien_trimmer v3.2 Adapter trimming for sequencing reads trimgalore v0.6.11 Wrapper for Cutadapt and FastQC for adapter trimming
Tool Latest Version Description canu v2.3 Long-read assembler savage v0.4.1 Sequence assembly for viral genomes spades v4.2.0 Assembly and analysis of sequencing data velvet v1.2.10 De novo genomic assembler
Tool Latest Version Description bayestraits v5.0.3 Bayesian analysis of trait evolution on phylogenies fastcodeml v1.1.0 Accelerated codeml for detecting positive selection hyphy v2.5.97 Hypothesis testing using phylogenies paml v4.8a Phylogenetic analysis by maximum likelihood pcoc v898c138 Detection of Convergent Amino-Acid Evolution pastml v1.9.51 Ancestral state reconstruction and phylogeographic inference
Tool Latest Version Description admixture v1.3.1 Maximum-likelihood estimation of individual ancestries finestructure v4.1.1 Population structure inference using haplotypes
Tool Latest Version Description deseq v1.39.0 Differential expression analysis from RNA-seq count data stringtie v2.2.1 Transcript assembly and quantification for RNA-seq subread v2.1.1 Subread/featureCounts read summarization for RNA-seq
Tool Latest Version Description checkm v1.2.5 Quality assessment of genome bins from metagenomes fastani v1.34 Fast and accurate whole-genome ANI estimation khmer v2.1.2 Probabilistic k-mer counting data structure kraken v2.17.1 Taxonomic classification of metagenomic sequences krakenuniq v1.0.4 Metagenomics classification using unique k-mer counts vamb v5.0.4 Variational autoencoders for metagenomic binning
Viral & Pandemic Analysis Tool Latest Version Description artic-ncov2019 e814ed4 ARTIC network bioinformatics tools for SARS-CoV-2 civet v2.1.2 Cluster investigation and virus epidemiology tool irma v1.3.1 Iterative refinement meta-assembler for viral genomics label v0.6.4 Sequence labeling and annotation tool nextstrain-base build-20251119T000157Z Nextstrain base environment for viral phylodynamics pangolin v4.4 Phylogenetic assignment of named global outbreak LINeages polecat b4a36f3 Phylogenetic Overview & Local Epidemiological Cluster Analysis Tool vivan v0.43 Virus variation analyzer
Tool Latest Version Description damageprofiler v1.1 Profiling damage patterns in ancient DNA reads mapdamage v2.2.3 Identifying and quantifying DNA damage in ancient DNA pathphynder v1.2.4 Ancient DNA placement into reference phylogenies schmutzi v1.5.6 Estimation of ancient DNA contamination
Tool Latest Version Description cd-hit v4.8.1 Sequence clustering gubbins v3.4.3 Rapid detection of recombination in bacterial genomes hmmer v3.4 Biosequence analysis using profile hidden Markov models jphmm v03.2015 Jumping profile hidden Markov model for HIV subtyping jphmm_tools v0.1.4 Tools for working with jpHMM output sdrmhunter v0.2.1.6 HIV surveillance drug resistance mutation identification
Tool Latest Version Description haploconduct v0.2.1 Haplotype-aware genome assembly toolkit haplogrep v2.4.0 Mitochondrial haplogroup classification predicthaplo v1.0 Predicting HIV haplotypes from next-generation sequencing shorah v1.99.3 Short Reads Assembly into Haplotypes strainline commit-8af032906e Full-length de novo viral haplotype reconstruction
Tool Latest Version Description indelible v1.03 Flexible evolutionary sequence simulator nanosim v3.2.3 Nanopore sequence read simulator seq-gen v1.3.5 Simulation of molecular sequence data along phylogenetic trees snag master Sequence simulation along a tree reseq 053b8d1 Realistic simulation of Illumina sequencing data
Tool Latest Version Description khmer v2.1.2 Probabilistic k-mer counting data structure musket v1.1 k-spectrum based short read error correction
Tool Latest Version Description igv v2.9.0 Integrative Genomics Viewer for alignment and variant data inkscape latest Vector graphics editor
Tool Latest Version Description snakemake v9.17.2 Workflow management system for reproducible bioinformatics
These images serve as base environments for building other images or running custom analyses:
Image Latest Version Description perl v5.32.1 Perl with BioPerl modules python v3.8.2 Python base image python-dl v3.13 Python with deep learning packages (TensorFlow, PyTorch) python-evol v3.8.2 Python with evolutionary biology packages python-ml v3.8.2 Python with machine learning packages r-base v4.0.2 R statistical computing base image r-evol v4.2.2 R with evolutionary biology packages r-extended v4.3.3 R with extended bioinformatics packages r-gisaid v4.1.2 R environment for GISAID data analysis r-sra v3.6.1 R environment for SRA data analysis ubuntu v24.04 Ubuntu base image
Tool Latest Version Description jq v1.8.1 Lightweight and flexible command-line JSON processor s3cmd v2.4.0 Command Line S3 Client and Backup for Linux and Mac s3utils v0.6.1 Utilities for interacting with Amazon S3 sphinx v1.8.5 Python documentation generator wget v1.17.1 Network utility to retrieve files from the Web
To build a Docker image from this repository, navigate to the tool's version directory and run docker build:
cd < tool-name> /< version> /
docker build -t evolbioinfo/< tool-name> :< version> . For example, to build the RAxML-NG image:
cd raxml-ng/v1.2.2/
docker build -t evolbioinfo/raxml-ng:v1.2.2 . Contributions of new Dockerfiles or updates to existing ones are welcome. Please follow the conventions used in this repository:
Place each tool's Dockerfile in a subdirectory named <tool-name>/<version>/. Use a LABEL maintainer= instruction to identify the image author. Use ENV VERSION=<version> to specify the tool version. Clean up build dependencies and package manager caches at the end of the RUN step. Define an ENTRYPOINT pointing to the tool's main executable where appropriate. Create a /pasteur directory at the end of the build (this is the shared mount point convention used in these images).