phylogeny.fr

2.1 "One Click" mode

This is a "default" mode which proposes a pipeline already set up to run and connect programs recognized for their accuracy and speed to reconstruct a robust phylogenetic tree from a set of sequences. The workflow depends on the chosen execution mode (Fast or Accurate):

• Mafft for rapid and robust multiple sequence alignment.
• Optionally ClipKit for alignment curation (trimming unreliable regions).
• FastTree (Fast mode) or IQ-TREE (Accurate mode) for phylogeny.

You have the ability to toggle the curation step (ClipKit) to eliminate poorly aligned positions and highly divergent regions before the tree inference step. At the end of the analysis, a beautiful, interactive rendition of the generated tree will be available for you to interact with and export.

Default Parameters

For transparency, below is the exhaustive list of the parameters used by the tools behind the scenes during a One Click run:

2.2 Advanced mode

The Advanced mode follows the same robust pipeline philosophy as "One Click" mode, utilizing a predefined succession of programs (Mafft, ClipKit, and FastTree). However, unlike One Click mode, it provides you with complete control over the parameters for each step of the analysis.

This mode is designed for intermediate to advanced users who want to fine-tune their phylogenetic reconstruction without dealing with the complex selection of individual tools from scratch.

2.3 "A la carte" mode

The "A la carte" mode provides the ultimate flexibility for building your phylogenetic analysis pipeline. Unlike the predefined workflows of One Click and Advanced modes, this mode allows you to handpick each tool for every step of the analysis, giving you complete control over your methodology.

Two-Phase Workflow

The A la carte mode operates in two distinct phases:

1. Pipeline Design: Select which tools you want to include in your analysis. A visual pipeline at the top of the page shows your current selection in real-time.
2. Configuration & Launch: After confirming your tool selection, configure each tool's parameters individually, upload your FASTA input, and submit the analysis.

Available Tools by Step

How It Works

1. Navigate to the A la carte page from the main menu.
2. Click on the tool tiles to select your preferred tool for each step (Alignment, Curation, Phylogeny). Selected tools are highlighted with a checkmark.
3. Click "Continue to Configuration" to proceed.
4. Upload your FASTA file or paste your sequences directly.
5. Configure each selected tool's parameters using the provided forms.
6. Optionally enter your email to receive a notification when the analysis completes.
7. Click "Submit Analysis" to start the pipeline.

3.1 Submitting a query

To run a BLAST search, you need to provide a single sequence in FASTA format. You can either upload a file or paste your sequence directly into the text area.

BLAST Programs

Select the appropriate program based on your query and target database types:

Available Databases

Choose from a variety of regularly updated sequence databases:

E-value Threshold

The E-value (Expect value) represents the number of hits you would expect to find by chance. A lower E-value indicates a more significant match:

• 1.e-5 (default): Good balance between sensitivity and specificity.
• 1.e-10 to 1.e-30: More stringent, returns only highly confident hits.
• 0.1 to 1: More permissive, may include distant homologs.

3.2 Interactive results

Once your BLAST job completes, you are presented with an interactive visualization combining a phylogenetic tree and a powerful floating Toolbox panel for filtering and exporting your results.

Phylogenetic Tree Display

The tree displays your query sequence alongside the top BLAST hits, allowing you to visualize evolutionary relationships at a glance:

• Query highlighting: Your input sequence is visually emphasized in the tree.
• Taxonomy coloring: Sequences are colored by taxonomic group (adjustable depth).
• Interactive selection: Click directly on tree leaves to select or deselect sequences.
• External links: Click on sequence IDs to access their original database entry.

The Toolbox Panel

The floating Toolbox is your control center for exploring BLAST results. It can be dragged anywhere on screen and offers two distinct modes via tabs:

Tree View Tab

This tab focuses on the top hits displayed in the phylogenetic tree (typically the best-scoring sequences). Use it for precise, small-scale selection:

• Selection counter: Shows how many sequences are currently selected out of total tree leaves.
• Quick select buttons: Instantly select all or deselect all sequences in the tree.
• Bitscore filter pills: Filter sequences by score ranges (<40, 40-50, 50-80, 80-200, >200) with color-coded pills.
• Taxonomy depth slider: Adjust the taxonomic classification level displayed (1=Kingdom to 8=Species level).
• Gap-free indicator: Shows the percentage of alignment positions without gaps for your current selection—useful for assessing alignment quality.

All Hits Tab

This tab operates on all BLAST hits, not just those in the tree. Use it for large-scale filtering across the entire result set:

• E-value threshold: Dynamically filter hits by E-value (from 1e-5 to 1e-100).
• Histogram filters: Open interactive histograms to select sequences by:
  • Score (bitscore): Filter by alignment score strength.
  • Similarity (% identity): Filter by sequence similarity percentage.
  • Coverage (% query coverage): Filter by how much of your query is covered.
• Taxonomy filter: Open a hierarchical taxonomy tree to select sequences from specific taxonomic groups (e.g., only Bacteria, only Vertebrates).
• Reset selection: Clear all filters and start fresh.

Exporting & Pipeline Integration

Both tabs provide export options for your selected sequences:

• Download FASTA: Export selected sequences as a FASTA file for external analysis.
• Send to Pipeline: Directly transfer selected sequences to the One Click or Advanced phylogeny pipelines. The sequences are automatically loaded into the analysis form.

Taxonomy Legend

Below the tree, a dynamic legend displays the taxonomic groups present in your results with their associated colors. The groups shown depend on the taxonomy depth setting in the Toolbox.