Infer a phylogenetic tree with bootstrap support
infer_treeBuild a maximum-likelihood tree and measure branch support via bootstrapping. Input aligned FASTA sequences and choose a substitution model.
Instructions
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.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| seed | No | ||
| fasta | Yes | ||
| model | No | GTR+G | |
| replicates | No | ||
| sequence_type | No | dna |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| model | Yes | ||
| engine | Yes | ||
| newick | Yes | ||
| support | Yes | ||
| warnings | Yes | ||
| alignment | Yes | ||
| log_likelihood | Yes | ||
| reproducibility | Yes | ||
| branch_length_units | Yes | ||
| newick_with_support | Yes |