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 v3.1.0
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 v3.3.20250515
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 v2.0.0
RAxML next-generation
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 v39.01
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
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 v1.46.2
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 v2.5.96
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 v2.0.3
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 v3.0.2
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 v4.3.1
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
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).