Infer a phylogenetic tree with bootstrap support
infer_treeBuild a maximum-likelihood phylogenetic tree from aligned sequences and quantify clade support with bootstrap replicates, choosing nonparametric or UFBoot2.
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.
support_method picks which bootstrap; see its entry for the cost.
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. Nonparametric: 20-1000, default 100,
and each one costs a full ML search, so the call takes about
replicates x one search. UFBoot2: 1000-10000, default 1000.
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.
fasta_path: Path of a FASTA file to read instead of fasta.
support_method: "bootstrap" (default): the nonparametric bootstrap,
clades supported at 0.70, and the only method that reports
well-supported clades the ML tree lacks (conflicting_support).
"ufboot": IQ-TREE's ultrafast bootstrap (UFBoot2, Hoang et al.
2018), clades supported at 0.95; far faster, use it when the
nonparametric cost (replicates x one ML search) is too high, e.g.
more than a few dozen taxa.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| seed | No | ||
| fasta | No | ||
| model | No | GTR+G | |
| fasta_path | No | ||
| replicates | No | ||
| sequence_type | No | dna | |
| support_method | No | bootstrap |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| model | Yes | ||
| engine | Yes | ||
| newick | Yes | ||
| support | Yes | ||
| warnings | Yes | ||
| alignment | Yes | ||
| log_likelihood | Yes | ||
| newick_topology | Yes | ||
| reproducibility | Yes | ||
| newick_supported | Yes | ||
| branch_length_units | Yes | ||
| newick_with_support | Yes |