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 sequences in FASTA, nucleotide or protein as declared by sequence_type. All sequences must be the same length — run align_sequences first if they are not. model: Substitution model, e.g. "JC", "HKY", "GTR+G" (or "LG+G" for protein). Run select_substitution_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: 0 to 2**31-1. Fixes the column resampling exactly; the engine's search is seeded too but is not bit-exact (see reproducibility). 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 sequences in FASTA, nucleotide or protein as declared by sequence_type. 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 a branch length on every edge. model: Substitution model to simulate under. A protein model ("LG", "WAG", ...) simulates protein; pass the output to infer_tree with sequence_type="protein". alignment.moltype says which it is. length: Number of sites. seed: Fixes the simulation.

Align unaligned sequences with MAFFT, ready for infer_tree.

The returned fasta has every row the same length and can be passed to infer_tree or select_substitution_model unchanged. Each output row, with its gaps removed, is verified to equal the input sequence before it is returned.

Args: fasta: UNALIGNED sequences in FASTA, 2-200 of them. Gap characters are refused: input that is already aligned does not need this tool. sequence_type: "dna" (default) or "protein". Declared, never sniffed, and passed to MAFFT explicitly so it does not guess either.

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

engine_version is the installed piqtree version (e.g. "0.8.3"); iqtree_version is the IQ-TREE build inside it (e.g. "3.1.2").

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