<!-- README.md is generated from README.Rmd. Please edit that file --> <img src="https://raw.githubusercontent.com/gkanogiannis/fastreeR/master/icon.png" alt="Project Icon" width="120"/> # fastreeR: Fast Tree Reconstruction Tools for Genomics <!-- badges: start -->     [](https://bioconductor.org/packages/release/bioc/html/fastreeR.html#since)[](http://bioconductor.org/packages/stats/bioc/fastreeR/) <!-- badges: end --> `fastreeR` is a hybrid toolkit combining a high-performance Java backend ([`BioInfoJava-Utils`](https://github.com/gkanogiannis/BioInfoJava-Utils)—a modular Java library for bioinformatics pipelines) with flexible and user-friendly interfaces across multiple platforms and environments, enabling seamless integration into a variety of genomic workflows. It enables fast computation of distance matrices and phylogenetic trees from genetic variant data in **VCF** or genomic sequences in **FASTA** format. ## Integration and Accessibility `fastreeR` offers interface, which is accessible in the following ways: - **NEW Java Backend (v2.y.z) !!** 100x times **FAST**re**ER** and only a couple hundred MB RAM needed. Java 11+ suggested. - ✅ **Bioconda**: install with `conda install -c bioconda fastreer` - ✅ **Docker**: available on [DockerHub](https://hub.docker.com/r/gkanogiannis/fastreer) and [GHCR](https://ghcr.io/gkanogiannis/fastreer) for containerized execution - ✅ **PyPI**: install with `pip install fastreer` - ✅ **Python CLI**: through a lightweight [Python wrapper](https://github.com/gkanogiannis/fastreeR/blob/devel/fastreeR.py) that calls the Java backend - ✅ **R / Bioconductor**: via `rJava` - ✅ **Galaxy**: Also available on Galaxy Toolshed. - ✅ **Pure Java API**: developers can integrate this library directly in Java-based pipelines or software. ------------------------------------------------------------------------ - [Key Features](#key-features) - [Requirements](#requirements) - [RAM Requirements](#memory-requirements-for-vcf-input) - [Installation and Usage](#installation-and-usage) - - [Conda](#via-conda) - [Docker](#via-docker) - [PyPI](#as-a-pypi-module) - [Python CLI](#via-a-python-cli-wrapper) - [R package](#as-an-r-package) - [Galaxy](#with-galaxy) - [From Java backend source](#from-java-backend-source) - [Distances from VCF](#distances-from-vcf) - [CLI Interface](#cli-interface) - [Commands](#commands) - [Examples](#examples) - [Options](#options-common-to-all-commands) - [Integration with Java Backend](#integration-with-java-backend) - [Integration with R](#integration-with-r) - [Sample data](#sample-data) - [Citation](#citation) - [Author](#author) - [License](#license) ------------------------------------------------------------------------ ## Key Features - 🚀 **Now ultra-fast with a superior multithreaded concurrency model and minimal RAM usage — from GBs down to just MBs!** - ⚡ Ultra-fast computation of sample-wise cosine distances from large VCF and D2S k-mer based distances from FASTA files. - 🌳 Generate agglomerative neighbor-joining phylogenetic trees directly from VCF or distance matrices. - 🧵 Multithreaded execution for speed and scalability. - Cluster distance matrices hierarchically with dynamic tree pruning. - 🧰 Clean Python CLI for scripting and pipeline integration - Streamlined integration with R via `rJava` - Available on Galaxy Toolshed - 🧬 Compatible with standard bioinformatics formats (PHYLIP, Newick) ------------------------------------------------------------------------ ## Requirements - Java 11+ (LTS version with improved concurrency) - Python 3.7+ - Maven (if you want to build from the source) - GNU/Linux, Windows or macOS ### Memory requirements for VCF input **No more GBs of RAM!** Only the distance matrix is kept in memory: - `4 bytes × (#samples²) × #threads` - Example: 1000 samples with 32 threads → **~128MB RAM** **VCF caching is minimal:** Only **2 VCF lines per thread** are pre-cached. - In the simple diploid case (e.g., `0/1`, `1|0`), each genotype requires ~4 characters (8 bytes). - For 1000 samples and 32 threads, this adds up to **~1MB RAM**. JVM will need at least 64-128 MB in order to efficiently run. **Total memory footprint: just a few hundred MB, even for large datasets.** ~~It is not straightforward to define a strict minimum amount of RAM required for a given number of SNPs and samples, as JVM behavior can vary across different systems and configurations. From our own experiments, a rough estimate for the minimum usable memory is around 10 bytes per variant per sample. For example, a VCF file with 1 million variants and 1,000 samples would require at least 10 × 10⁶ × 10³ = 10 GB of allocated memory. However, running with this minimal allocation may result in frequent and prolonged garbage collection events, leading to significantly longer runtimes. For optimal execution, we recommend allocating 15–20 bytes per variant per sample (i.e., 15–20 GB for the same example), which reduces garbage collection overhead and ensures smoother performance.~~ In order to allocate RAM, a special parameter needs to be passed while JVM initializes. JVM parameters can be passed by setting `java.parameters` option. The `-Xmx` parameter, followed (without space) by an integer value and a letter, is used to tell JVM what is the maximum amount of heap RAM that it can use. The letter in the parameter (uppercase or lowercase), indicates RAM units. For example, parameters `-Xmx1024m` or `-Xmx1024M` or `-Xmx1g` or `-Xmx1G`, all allocate 1 Gigabyte or 1024 Megabytes of maximum RAM for JVM. In order to allocate 1024MB of RAM for the JVM, through R code, use: ``` r options(java.parameters = "-Xmx1024M") ``` When using `fastreeR` as a CLI, then RAM allocation in MB can be achieved with the relevant argument `--mem MEM`. ------------------------------------------------------------------------ ## Installation and Usage ### Via Conda ``` bash conda create -y -n fastreer-env -c bioconda fastreer && activate fastreer-env fastreeR --help ``` ### Via Docker `fastreeR` is available as a lightweight, multithreaded, platform-independent Docker image hosted on both **DockerHub** and **GHCR**. From DockerHub: ``` bash docker pull gkanogiannis/fastreer:latest ``` Or from GitHub Container Registry (GHCR): ``` bash docker pull ghcr.io/gkanogiannis/fastreer:latest ``` To compute a tree directly from a VCF file: ``` bash docker run --rm -v $(pwd):/data gkanogiannis/fastreer:latest \ VCF2TREE -i /data/input.vcf -o /data/output.nwk --threads 4 ``` This: \* Mounts your working directory `$(pwd)` inside the container \* Reads `input.vcf` and writes `output.nwk` relative to your host \* Uses 4 threads for faster computation The Docker image includes: \* Java 17 \* Python3 \* All required `.jar` libraries \* The `fastreeR.py` CLI entry point Example: FASTA to distance ``` bash docker run --rm -v $(pwd):/data gkanogiannis/fastreer \ FASTA2DIST -i /data/sequences.fasta -o /data/sequences.dist -k 4 -t 2 ``` Memory tuning Use the `--mem` option to control how much memory is allocated to the Java backend: ``` bash docker run --rm -v $(pwd):/data gkanogiannis/fastreer \ VCF2TREE -i /data/input.vcf -o /data/output.nwk --mem 128 ``` > Internally, this sets the Java heap to `-Xmx128G`. ### As a PyPI Module You can install the Python CLI directly from PyPI using: ``` bash pip install fastreer ``` This will install the fastreeR command-line tool (`fastreer`) and include the Java backend jars required for running all commands. To check it installed correctly: ``` bash fastreeR --version ``` ### Via a Python CLI wrapper Another easy method for using `fastreeR` is by its Python CLI: ``` bash git clone https://github.com/gkanogiannis/fastreeR.git python fastreeR/fastreeR.py ``` Note: If you want to use a custom backend location, set the environment variable `FASTREER_JAR_DIR`. ### As an R package To install `fastreeR` as an R package: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("fastreeR") ``` You can install the development version of `fastreeR` R package like so: ``` r devtools::install_github("gkanogiannis/fastreeR") ``` ### With Galaxy Search in Galaxy Tools for `fastreer` or ask your Galaxy Admin to install it from toolshed. ### From java backend source To build the Java backend from source code: ``` bash git clone https://github.com/gkanogiannis/fastreeR.git git clone https://github.com/gkanogiannis/BioInfoJava-Utils.git pushd BioInfoJava-Utils mvn clean initialize package && popd ``` Then copy the resulting `.jar` file(s) to the `fastreeR/inst/java/` directory: ``` bash cp BioInfoJava-Utils/bin/*.jar fastreeR/inst/java/ ``` Finally run the tool from its Python CLI: ``` bash python fastreeR/fastreeR.py ``` ------------------------------------------------------------------------ ## Distances from VCF Calculates a cosine type dissimilarity measurement between the `n` samples of a VCF file. Biallelic or multiallelic (maximum 7 alternate alleles) SNP and/or INDEL variants are considered, phased or not. Some VCF encoding examples are: - heterozygous variants : `1/0` or `0/1` or `0/2` or `1|0` or `0|1` or `0|2` - homozygous to the reference allele variants : `0/0` or `0|0` - homozygous to the first alternate allele variants : `1/1` or `1|1` If there are `n` samples and `m` variants, an `nxn` zero-diagonal symmetric distance matrix is calculated. The calculated cosine type distance (1-cosine_similarity)/2 is in the range `[0,1]` where value `0` means completely identical samples (cosine is `1`), value `0.5` means perpendicular samples (cosine is `0`) and value 1 means completely opposite samples (cosine is `-1`). The calculation is performed by a Java back-end implementation, that supports multi-core CPU utilization and can be demanding in terms of memory resources. Output distances is a PHYLIP compatible file will contain `n+1` lines. The first line contains the number `n` of samples and number `m` of variants, separated by space. Each of the subsequent `n` lines contains `n+1` values, separated by space. The first value of each line is a sample name and the rest `n` values are the calculated distances of this sample to all the samples. Example output file of the distances of 3 samples calculated from 1000 variants: | 3 1000 | | | | |---------|-----|-----|-----| | Sample1 | 0.0 | 0.5 | 0.2 | | Sample2 | 0.5 | 0.0 | 0.9 | | Sample3 | 0.2 | 0.9 | 0.0 | ------------------------------------------------------------------------ ## CLI Interface The Python CLI (`fastreeR.py`) interfaces with the Java backend via `subprocess`, providing a unified command-line interface for all supported tools. ### Commands #### General Syntax ``` bash python3 fastreeR.py <COMMAND> [OPTIONS] ``` | COMMAND | Description | |--------------|--------------------------------------------------| | `VCF2DIST` | Compute a cosine distance matrix from a VCF file | | `VCF2TREE` | Compute a Newick NJ tree directly from a VCF | | `DIST2TREE` | Compute a Newick NJ tree from a distance matrix | | `FASTA2DIST` | Compute a D2S distance matrix from a FASTA file | ------------------------------------------------------------------------ ### Examples #### Compute Distance Matrix from VCF ``` bash python fastreeR.py VCF2DIST -i input.vcf -o output.dist --threads 16 --verbose ``` #### Compute Newick NJ tree directly from a VCF file. ``` bash python fastreeR.py VCF2TREE -i input.vcf -o output.nwk --threads 16 --verbose ``` #### Compute Tree from Distance Matrix ``` bash python fastreeR.py DIST2TREE -i output.dist -o output.nwk ``` **Input format:** tab-separated PHYLIP-compatible matrix. ### Compute D2S k-mer distance matrix from a FASTA file. ``` bash python3 fastreeR.py FASTA2DIST -i seqs.fasta -o output.dist -k 4 -t 2 --normalize ``` #### Pipe input from gzip-compressed file ``` bash zcat input.vcf.gz | python fastreeR.py VCF2TREE -i - -o output.nwk ``` #### Print version and citation ``` bash python fastreeR.py --version ``` ### Output Examples - Distance matrices: PHYLIP-compatible text - Trees: Newick format - Output is streamed line-by-line (suitable for large datasets) ------------------------------------------------------------------------ ### Options (common to all commands) - `-i, --input` : Input file (VCF or distance matrix). Use `-` for stdin. - `-o, --output` : Output file. If omitted, prints to stdout. - `-t, --threads` : Number of threads (default: 1). - `--mem MEM` : Max RAM for JVM in MB (default: 256). - `--lib LIB` : Path to the folder containing backend JAR libraries (default: inst/java) - `--verbose` : Print progress information to stderr. - `--pipe-stderr` : Pipe stderr and forward from Python (default: direct passthrough to terminal). - `--version` : Print version and citation information. ------------------------------------------------------------------------ ## Integration with Java Backend The CLI wraps tools from the [BioInfoJava-Utils](https://github.com/gkanogiannis/BioInfoJava-Utils) project and dynamically builds the Java classpath from all `.jar` files located in `inst/java/`. ------------------------------------------------------------------------ ## Integration with R All core functionality is available via the `fastreeR` R package (Bioconductor/devel): ``` r library(fastreeR) tree <- vcf2tree("input.vcf") plot(tree) ``` See [fastreeR R manual](https://www.bioconductor.org/packages/release/bioc/manuals/fastreeR/man/fastreeR.pdf) and [fastreeR R vignette](https://www.bioconductor.org/packages/release/bioc/vignettes/fastreeR/inst/doc/fastreeR_vignette.html) for usage in R. ------------------------------------------------------------------------ ## Sample data Toy vcf, fasta and distance sample data files are provided in `inst/extdata`. ### samples.vcf.gz Sample VCF file of 100 individuals and 1000 variants, in Chromosome22, from the 1K Genomes project. Original file available at <http://hgdownload.cse.ucsc.edu/gbdb/hg19/1000Genomes/phase3/> ``` r vcfFile <- system.file("extdata", "samples.vcf.gz", package = "fastreeR") ``` ### samples.vcf.dist.gz Distances from the previous sample VCF ``` r vcfDist <- system.file("extdata", "samples.vcf.dist.gz", package = "fastreeR") ``` ### samples.vcf.istats Individual statistics from the previous sample VCF ``` r vcfIstats <- system.file("extdata", "samples.vcf.istats", package = "fastreeR") ``` ### samples.fasta.gz Sample FASTA file of 48 random bacteria RefSeq from <ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/> . ``` r fastaFile <- system.file("extdata", "samples.fasta.gz", package = "fastreeR") ``` ### samples.fasta.dist.gz Distances from the previous sample FASTA ``` r fastaDist <- system.file("extdata", "samples.fasta.dist.gz", package = "fastreeR") ``` ------------------------------------------------------------------------ ## Citation If you use `fastreeR` in your research, please cite: > **Anestis Gkanogiannis (2016)** > *A scalable assembly-free variable selection algorithm for biomarker > discovery from metagenomes* > BMC Bioinformatics 17, 311. > <https://doi.org/10.1186/s12859-016-1186-3> > <https://github.com/gkanogiannis/fastreeR> ------------------------------------------------------------------------ ## Author **Anestis Gkanogiannis** Website: <https://www.gkanogiannis.com> ORCID: [0000-0002-6441-0688](https://orcid.org/0000-0002-6441-0688) ------------------------------------------------------------------------ ## License `fastreeR` is licensed under the GNU General Public License v3.0. See the [LICENSE](LICENSE) file for details. ------------------------------------------------------------------------