RaMAx

RaMAx aligns multiple genomes and produces whole‑genome alignments in standard formats. Its input and output conventions are compatible with [Cactus] (i.e., it accepts the same seqfile style input and can emit MAF and HAL alignments), so you can drop RaMAx into existing Cactus‑based workflows with minimal changes.

If you already have a Cactus seqfile, you can pass it directly to RaMAx.

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Build from Source

Prerequisites (Ubuntu/Debian)

Install the following packages first:

sudo apt update
sudo apt install -y \
    build-essential \
    cmake \
    libcurl4-openssl-dev \
    zlib1g-dev \
    libhdf5-dev

Notes

• libhdf5-dev is required for HAL support.
• On non‑Debian systems, install the equivalent development packages for CMake, libcurl, zlib, and HDF5.

Build Steps

# Clone the repository (with submodules)
git clone https://github.com/metaphysicser/RaMAx --recursive
cd RaMAx

# Create a build directory
mkdir build && cd build

# Configure
cmake ..

# Build using all available CPU cores
make -j"$(nproc)"

After a successful build, the executable ramax will be located in the build/ directory.

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Quick Start

Basic usage

./ramax \
  -i <path/to/seqfile.txt> \
  -o <path/to/output.{maf|hal}> \
  -w <path/to/workdir> \
  -t <threads>

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Command‑line Options (common)

Flag	Description
-i <file>	Input seqfile (same format used by Cactus).
-o <file>	Output alignment path. RaMAx supports MAF and HAL.
-w <dir>	Working directory to store intermediate files and logs (created if missing).
-t <N>	Number of worker threads to use.

Input format (seqfile)

RaMAx uses the same seqfile format as Cactus. The file has two parts:

1. A species tree in Newick on the first non‑comment line (leaf names must match genomes below; branch lengths optional).
2. Genome mappings, one per line: <genome_name> <path/to/genome.{fa|fasta|fa.gz}>.

Minimal example

# seqfile.txt
# 1) Species tree (Newick)
((human:0.005,chimp:0.005):0.02,orangutan:0.025);

# 2) Genome mappings (one per leaf)
human      /data/genomes/hg38.fa
chimp      /data/genomes/panTro6.fa
orangutan  /data/genomes/ponAbe3.fa.gz

Output formats RaMAx can write MAF for broad downstream compatibility and HAL for hierarchical alignment workflows.