Documentation

Table of Content

1. Overview
2. Phylogeny Analysis
3. Blast: Sequence Explorer
4. Programs use and technical details
5. Formats
6. More information about external software
Viewing and downloading results
References
Job expiration and deletion

1. Overview

phylogeny.atgc-montpellier.fr connects alignment, curation, phylogenetic inference and tree display in one workflow. Choose One Click for the standard pipeline, Advanced to configure its stages, or A la Carte to select different methods. The Online Programs page also provides individual tools.

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2. Phylogeny Analysis

2.1 "One Click" mode

One Click constructs a tree from a set of DNA or protein sequences. Sequence type is detected automatically. MUSCLE aligns the sequences, optional Gblocks curation removes poorly aligned positions, PhyML infers the tree, and the TreeDyn replacement displays it. FASTA, EMBL, GenBank, NEXUS, CLUSTAL and PHYLIP sequence inputs are accepted and normalized before alignment.

2.2 Advanced mode

Advanced uses the same processing stages with configurable parameters. Select the first and last stages to run: an alignment-only analysis, curation of an existing alignment, inference from an alignment, and rendering an existing tree are also available.

2.3 "A la Carte" mode

A la Carte lets you choose the alignment and phylogeny methods independently, omit curation, and set each method's parameters. A tree-rendering stage requires a tree as input; an alignment must first pass through a phylogeny method.

With step by step, the workflow pauses after each completed stage. Review and download its results, then select Continue to next step. The Edit next step data and settings link lets you replace the input data or adjust the next method's parameters before continuing. With all at once, the selected stages run in sequence automatically.

Input data and names

Upload one text file or paste its content. Do not use both input methods together. Every sequence must have a unique identifier. An alignment must contain sequences of equal length, including gaps. At least three sequences are needed for phylogenetic inference; MrBayes requires at least four.

The Names association block maps short identifiers to readable taxon labels. Enter one current identifier and corresponding replacement label per line. These labels are applied in tree rendering, leaving the alignment identifiers unchanged.

To prepare a file for another program, use the Built-in converter. It converts sequence alignments and trees between standard formats. PHYLIP with long names preserves identifiers; strict PHYLIP rejects names longer than ten characters. An output format may not support all annotations in its source format.

3. Blast: Sequence Explorer

The BLAST page searches Swiss-Prot or an uploaded FASTA database. Swiss-Prot is a protein database (BLASTP or BLASTX). For other databases, use NCBI BLAST.

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4. Programs use and technical details

Online Programs includes MUSCLE, ClustalW, T-Coffee, ProbCons, 3DCoffee / Expresso, Gblocks, the built-in gap-column curer, PhyML, FastME, MrBayes, TNT, ASTRAL, SMS, Readseq, Jalview and tree viewers.

ProbCons retains probabilistic consistency alignment, including the original nucleotide variant. Expresso performs structure-guided alignment using supplied PDB templates or automatic template discovery. Structural searches depend on upstream structure databases.

FastME supplies distance-based phylogeny with explicit algorithm and tree-refinement choices. Separate BioNJ and Neighbor tools provide distance-based trees without the additional FastME refinement; they also expose bootstrap sampling.

TNT is available behind a license-agreement gate. Read and accept the official license before submitting a standalone or A la Carte analysis.

Jalview opens FASTA alignments in an embedded JalviewJS client. Use the editor's FASTA or CLUSTAL export buttons to save changes before leaving the page. The separate FASTA and .jvl launch downloads preserve the original alignment and are also available if the embedded client cannot load.

Viewing and downloading results

Keep the analysis URL to return to its status and results. The page refreshes while computation runs, displays errors when a tool fails, and provides downloads for completed stages. Processing continues when the browser is closed.

TreeDyn and ATV support rectangular, cladogram, circular and unrooted layouts. Load a tree to search its names or annotations, select a node, collapse or expand branches, view a subtree, change descendant order, reroot or edit node information. The display controls include gene names, accessions, taxonomy, branch values, orthology colors and NHX protein domains. Reopen a saved tree to continue editing. SVG, PNG, PDF, PS, EPS, Newick, NEXUS and NHX downloads are provided. The original input remains unchanged; explicit edits are saved in the complete exported tree. A displayed subtree has its own separate download, and hiding annotations or domains does not remove their data.

Your Workspace lists recent analyses from this browser. Signing in associates earlier anonymous analyses from this browser with your account. Password recovery uses the email address entered during registration.

Email notification is optional; up to five recipient addresses can be separated by commas. In One Click, the attachment checkbox controls whether result files accompany the email; the result URL is included either way.

5. Formats

Paste sequence data or upload a plain-text file. FASTA is usually the simplest choice. Use the Built-in converter or Readseq when another format is needed. Alignments must contain equally long sequences, including gaps.

5.1 FASTA format

Each sequence begins with a line starting with > and a unique identifier. Sequence characters follow on one or more lines.

>Taxon_A
ACGTAC
>Taxon_B
ACGTTC
>Taxon_C
ACGGAC

5.2 GenBank format

A GenBank record contains a LOCUS line, descriptive and feature fields, and an ORIGIN sequence section. A line containing // ends each record. Export the complete record as plain text; a web page displaying the record is not a sequence file.

5.3 EMBL format

An EMBL record begins with ID, stores annotations in tagged lines and sequences after SQ, and ends with //. Keep the complete record when importing annotated data.

5.4 PHYLIP format

The first line gives the number of sequences and alignment length. Each sequence has a name and aligned residues. Strict PHYLIP reserves ten characters for names; the relaxed variant supports longer identifiers.

3 6
Taxon_A   ACGTAC
Taxon_B   ACGTTC
Taxon_C   ACGGAC

5.5 Clustal format

A Clustal alignment begins with a CLUSTAL header and presents named sequences in aligned blocks. Optional conservation lines describe the alignment.

CLUSTAL W multiple sequence alignment

Taxon_A   ACGTAC
Taxon_B   ACGTTC
Taxon_C   ACGGAC

5.6 NEXUS format

NEXUS uses named blocks. This example contains an aligned DNA data matrix; tree data use a separate TREES block.

#NEXUS
BEGIN DATA;
  DIMENSIONS NTAX=3 NCHAR=6;
  FORMAT DATATYPE=DNA MISSING=? GAP=-;
  MATRIX
  Taxon_A ACGTAC
  Taxon_B ACGTTC
  Taxon_C ACGGAC
  ;
END;

Tree viewers also accept Newick trees, such as ((Taxon_A:0.1,Taxon_B:0.2):0.3,Taxon_C:0.4);. See each form for its accepted formats.

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6. More information about external software

MAFFT and Clustal Omega align sequences. BMGE and ClipKit trim existing alignments. IQ-TREE 3, RAxML-NG and FastTree infer trees.

IQ-TREE's automatic model uses ModelFinder; RAxML-NG's automatic choice uses GTR+G for DNA and LG+G for proteins. FastTree reports SH-like local support, which differs from conventional bootstrap proportions. These programs are available individually from Online Programs. Download their output to use it in another tool.

Reactree provides tree editing and an optional synchronized alignment. ReSeqt provides alignment coloring, conservation, search, zoom and image export. Both viewers are served locally under their MIT license and do not send data to the developers' website.

Program versions, selected parameters and diagnostic logs accompany analysis results.

References

Please cite Dereeper et al., Phylogeny.fr: robust phylogenetic analysis for the non-specialist, Nucleic Acids Research (2008), and each scientific program used. The Downloads page links to the programs and sample data.

Job expiration and deletion

Current policy: 30 days from submission, including time spent waiting or computing. Your Workspace and each result page show the exact expiration date recorded for that analysis. Download the files you need before that date; this site is not a permanent archive.

At expiration, the job becomes Expired. Results, previews and downloads become inaccessible, and local input, intermediate and output files are removed in the background. There is no recovery period offered by this site. A history record remains with the analysis name, owner, dates and status; expiration does not delete your account or copies already downloaded or kept in backups.

Use Delete in your workspace or on a result page to expire one of your jobs immediately, after confirmation. For anonymous submissions, deletion is available only from the browser session that submitted the job. For an account-owned analysis, its owner must be signed in.

A Delete request also queues expiration of all associated computation steps. If the request cannot be completed immediately, it is retried automatically. This does not guarantee that a running calculation stops immediately or that files on the computation servers are immediately erased: those copies follow a separate retention policy. Automatic expiration here after 30 days removes the copies stored on this site; it does not request expiration on the computation servers.

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phylogeny.atgc-montpellier.fr is provided by the ATGC bioinformatics platform.