dadaist2

Dadaist2-tree

A phylogenetic tree generation tool optimized for metabarcoding data (16S rRNA and ITS sequences), that takes representative-sequences.fasta and generates a tree.nwk file (Newick format).

usage: dadaist2-tree [-h] -i INPUT -o OUTPUT [-t THREADS] [--marker {16S,ITS}] [--fast]

Generate phylogenetic tree from metabarcoding (16S/ITS) sequences

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input FASTA file containing ASVs/OTUs (default: None)
  -o OUTPUT, --output OUTPUT
                        Output tree file (Newick format) (default: None)
  -t THREADS, --threads THREADS
                        Number of threads to use (default: 1)
  --marker {16S,ITS}    Marker gene type (affects alignment parameters) (default: 16S)
  --fast                Use fast mode (Clustal Omega + FastTree) instead of MAFFT + IQ-TREE (default: False)

Features

• Multiple sequence alignment using either MAFFT (standard mode) or Clustal Omega (fast mode)
• Phylogenetic tree construction using either IQ-TREE (standard mode) or FastTree (fast mode)
• Optimized parameters for both 16S rRNA and ITS marker genes
• Multi-threaded operations for faster processing
• Rich logging with progress indicators

Installation

Dependencies

The program requires the following external tools to be installed and available in your PATH:

Standard mode:

• MAFFT
• IQ-TREE

Fast mode:

• Clustal Omega
• FastTree

Python Dependencies

pip install rich

Usage

Basic usage:

python dadaist2-tree.py -i input.fasta -o output.tree -t 4

All options:

python dadaist2-tree.py [-h] -i INPUT -o OUTPUT [-t THREADS] [--marker {16S,ITS}] [--fast]

Arguments

• -i, --input: Input FASTA file containing ASVs/OTUs (required)
• -o, --output: Output tree file in Newick format (required)
• -t, --threads: Number of threads to use (default: 1)
• --marker: Marker gene type, either ‘16S’ or ‘ITS’ (default: 16S)
• --fast: Use fast mode (Clustal Omega + FastTree) instead of MAFFT + IQ-TREE

Marker Type Selection (–marker)

The --marker option optimizes the alignment parameters based on the type of sequences being analyzed:

16S rRNA (–marker 16S)

For 16S rRNA sequences, the program uses:

• MAFFT with FFT-NS-2 algorithm
• Adjusted gap penalties (op = 1.53, ep = 0.123)
• Lower number of iterations
• Suitable for sequences with high similarity and conserved structure

This configuration is optimized for:

• Shorter sequences (typically ~1500 bp)
• More conserved regions
• Lower gap frequency
• Higher sequence similarity

ITS (–marker ITS)

For ITS (Internal Transcribed Spacer) sequences, the program uses:

• MAFFT with E-INS-i algorithm
• Increased number of iterations (up to 1000)
• Better handling of multiple conserved domains
• More sensitive gap handling

This configuration is optimized for:

• More variable sequence lengths
• Higher sequence divergence
• Multiple conserved domains interrupted by variable regions
• Higher gap frequency

Modes of Operation

Standard Mode (Default)

Uses MAFFT for alignment and IQ-TREE for phylogenetic inference:

• More accurate but slower
• Includes statistical support values (ultra-fast bootstrap)
• Automatically selects best evolutionary model
• Recommended for publication-quality trees

# Standard mode example
python dadaist2-tree.py -i input.fasta -o output.tree -t 4 --marker 16S

Fast Mode

Uses Clustal Omega for alignment and FastTree for phylogenetic inference:

• Faster but potentially less accurate
• Good for quick exploratory analysis
• Uses GTR model with optimization
• Suitable for large datasets where computational time is a concern

# Fast mode example
python dadaist2-tree.py -i input.fasta -o output.tree -t 4 --fast

Output

The program generates a phylogenetic tree in Newick format. In standard mode, the tree includes:

• Branch lengths
• Ultra-fast bootstrap support values (standard mode only)
• SH-aLRT test values (standard mode only)

Error Handling

The program includes:

• Dependency checking
• Input file validation
• Rich error messaging
• Temporary file cleanup
• Progress logging

Contributing

Feel free to submit issues and enhancement requests!

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