.. _raxml-ng:

========
RAxML-NG
========

.. contents:: In this section:
   :local:
   :depth: 2

Description
===========

According to the `page of RAxML-NG <https://github.com/amkozlov/raxml-ng>`_, RAxML-NG is a phylogenetic inference tool using the maximum likelihood (ML) optimality criterion. It is the successor to RAxML, offering improvements in speed, flexibility, and usability.

Available Versions
==================

* raxml-ng/1.0.3 (default)

Loading the Module
==================

.. code-block:: bash

   # Load RAxML-NG
   module load raxml-ng/1.0.3

   # Verify installation
   raxml-ng --version
   raxml-ng-mpi --version

Job Submission
==============

.. code-block:: bash
   :caption: submit_raxml-ng.sh

   #!/bin/bash
   #SBATCH -J raxmlng
   #SBATCH -N 1
   #SBATCH -c 8
   #SBATCH -t 24:00:00
   #SBATCH --mem=16G

   export INPUT="test.fa"
   export OUTPUT="test.fa.raxml.*"

   module load raxml-ng/1.0.3

   job-nanny raxml-ng --msa test.fa --model GTR+G --threads $SLURM_CPUS_PER_TASK

Best Tree Search
================

.. code-block:: bash
   :caption: submit_raxml-ng_search.sh

   #!/bin/bash
   #SBATCH -J raxmlng_search
   #SBATCH -N 1
   #SBATCH -c 8
   #SBATCH -t 48:00:00
   #SBATCH --mem=32G

   export INPUT="alignment.phy"
   export OUTPUT="RAxMLNG_*"

   module load raxml-ng/1.0.3

   job-nanny raxml-ng --msa alignment.phy --model GTR+G \
                    --threads $SLURM_CPUS_PER_TASK \
                    --prefix RAxMLNG --seed 12345

Bootstrap
=========

.. code-block:: bash
   :caption: submit_raxml-ng_bootstrap.sh

   #!/bin/bash
   #SBATCH -J raxmlng_boot
   #SBATCH -N 1
   #SBATCH -c 8
   #SBATCH -t 72:00:00
   #SBATCH --mem=32G

   export INPUT="alignment.phy"
   export OUTPUT="RAxMLNG_*"

   module load raxml-ng/1.0.3

   # Bootstrap
   job-nanny raxml-ng --bootstrap --msa alignment.phy --model GTR+G \
                    --threads $SLURM_CPUS_PER_TASK \
                    --prefix boot --seed 12345 --bs-trees 100

   # Map bootstrap on best tree
   job-nanny raxml-ng --support --tree boot.raxml.bestTree \
                    --bs-trees boot.raxml.bootstraps \
                    --prefix support --threads $SLURM_CPUS_PER_TASK

Full Analysis (Search + Bootstrap)
==================================

.. code-block:: bash
   :caption: submit_raxml-ng_all.sh

   #!/bin/bash
   #SBATCH -J raxmlng_all
   #SBATCH -N 1
   #SBATCH -c 8
   #SBATCH -t 96:00:00
   #SBATCH --mem=32G

   export INPUT="alignment.phy"
   export OUTPUT="RAxMLNG_*"

   module load raxml-ng/1.0.3

   job-nanny raxml-ng --all --msa alignment.phy --model GTR+G \
                    --threads $SLURM_CPUS_PER_TASK \
                    --prefix complete --seed 12345 \
                    --bs-trees 100

Available Models
================

.. list-table:: Evolution Models
   :header-rows: 1
   :widths: 20 80

   * - Model
     - Description
   * - ``GTR+G``
     - General Time Reversible with gamma distribution
   * - ``GTR+G4``
     - GTR with 4 gamma categories
   * - ``GTR+I+G4``
     - GTR with invariant proportion + gamma
   * - ``JC69``
     - Jukes-Cantor 1969
   * - ``HKY85``
     - Hasegawa-Kishino-Yano 1985
   * - ``TN93``
     - Tamura-Nei 1993
   * - ``K80``
     - Kimura 2-parameter
   * - ``F81``
     - Felsenstein 1981

Job Array for Multiple Alignments
=================================

.. code-block:: bash
   :caption: submit_raxml-ng_array.sh

   #!/bin/bash
   #SBATCH -J raxmlng_array
   #SBATCH --array=1-10
   #SBATCH -N 1
   #SBATCH -c 8
   #SBATCH -t 48:00:00
   #SBATCH --mem=32G

   FILES=($(ls *.phy *.fa *.fasta))
   FILE=${FILES[$SLURM_ARRAY_TASK_ID-1]}
   PREFIX="raxmlng_${FILE%.*}"

   export INPUT="$FILE"
   export OUTPUT="${PREFIX}_*"

   module load raxml-ng/1.0.3

   job-nanny raxml-ng --msa $FILE --model GTR+G \
                    --threads $SLURM_CPUS_PER_TASK \
                    --prefix $PREFIX --seed 12345

Results Analysis
================

.. code-block:: bash
   :caption: analyze_raxml-ng.sh

   #!/bin/bash
   #SBATCH -J analyze_raxmlng
   #SBATCH -N 1
   #SBATCH -n 1
   #SBATCH -t 01:00:00
   #SBATCH --mem=4G

   module load raxml-ng/1.0.3

   # Check bootstrap convergence
   raxml-ng --bsconvergence --bs-trees boot.raxml.bootstraps \
            --prefix convergence --seed 12345

   # Calculate consensus tree
   raxml-ng --consense --tree boot.raxml.bootstraps \
            --prefix consense --seed 12345

   # Extract statistics
   for f in *.raxml.log; do
       echo "File: $f"
       grep "Final log likelihood" $f
       grep "Tree length" $f
       grep "Number of distinct tree topologies" $f
       echo "---"
   done > stats.txt

   # Generate tree PDF (requires Python with ete3)
   cat > plot_tree.py << 'EOF'
   from ete3 import Tree, TreeStyle
   import glob

   for tree_file in glob.glob("*.raxml.bestTree"):
       t = Tree(tree_file)
       ts = TreeStyle()
       ts.show_leaf_name = True
       ts.show_branch_length = True
       ts.show_branch_support = True
       
       outfile = tree_file.replace("bestTree", "tree.pdf")
       t.render(outfile, tree_style=ts)
   EOF

   python plot_tree.py 2>/dev/null || echo "ete3 not installed"

References
==========

- Documentation: https://github.com/amkozlov/raxml-ng/wiki
- Manual: https://github.com/amkozlov/raxml-ng/blob/master/README.md
- Tutorial: https://github.com/amkozlov/raxml-ng/wiki/Tutorial

.. seealso::

   - :ref:`raxml` - Previous version
   - :ref:`beast` - Bayesian analysis
   - :ref:`exabayes` - Bayesian alternative
   - :ref:`running_simulations` - How to submit jobs