Build a maximum-likelihood tree and measure how well the data support it.

Always bootstraps. There is deliberately no option to skip it: an unsupported topology is the failure mode this server exists to prevent.

Args: fasta: Aligned nucleotide sequences in FASTA. All sequences must be the same length — this server does not align. model: Substitution model, e.g. "JC", "HKY", "GTR+G". Run select_model first if you do not have a reason to prefer one. replicates: Bootstrap replicates (20-1000). Cost is roughly linear in this, so 100 is a reasonable default and 1000 is for a final answer. seed: Fixes both the resampling and the engine's search. sequence_type: "dna" (default) or "protein". DECLARED, never sniffed: an alignment of only A/C/G/T is a valid protein alignment too, so guessing would silently fit a nucleotide model to protein data. A protein alignment also needs a protein model — "LG+G" or "WAG", not the nucleotide default — so run select_substitution_model with the same sequence_type first.

Compare substitution models and report how much the winner won by.

A single model name reads as a finding. The ranking, the delta to the next model, and whether AIC/AICc/BIC agree are what make it one.

Args: fasta: Aligned nucleotide sequences in FASTA. criterion: "AIC", "AICc" or "BIC". BIC penalises parameters more heavily. seed: Fixes the engine's search. top_n: How many ranked models to return. sequence_type: "dna" (default) or "protein". Ranks within that molecule type's model set — nucleotide and protein models are not comparable.

Robinson-Foulds distance between two trees, and which clades differ.

Compares SPLITS, not strings: the same topology has many valid Newick representations, so string equality answers a different question.

Args: newick_a: First tree in Newick format. newick_b: Second tree in Newick format.

Generate sequences along a tree you specify, so the true answer is known.

This is the positive control for everything else here: infer a tree from the output and compare it back with compare_trees. If inference cannot recover a topology you generated from, the problem is the data or the settings, not the biology.

Args: newick: The true tree, with branch lengths. model: Substitution model to simulate under. length: Number of sites. seed: Fixes the simulation.

What this server can do, and the bounds it enforces.

Args: include_models: Include the full substitution-model list (long).