---
title: "Phylogenetic tree (neighbour-joining, with bootstrap)"
method: POST
path: "/phylogenetic_tree"
tags: ["Alignment & variants"]
---

# Phylogenetic tree (neighbour-joining, with bootstrap)

`POST /phylogenetic_tree`

## Request

- Base URL: `https://seqbench.com/api/v1`
- URL: `https://seqbench.com/api/v1/phylogenetic_tree`
- Auth: none required

A neighbour-joining tree from a multiple ALIGNMENT, as Newick. Distances are corrected pairwise identities over the columns where both rows have a residue — Jukes-Cantor for nucleotides, Poisson for protein, the same corrections MEGA applies by default — and the tree is rooted at the midpoint of its longest tip-to-tip path. Branch support is Felsenstein's bootstrap over alignment columns, written into the Newick as the usual internal-node labels and returned per split; it needs four or more sequences and is refused with a reason past the work one call will do, rather than returned from fewer replicates under the same name. Takes the output of multiple_sequence_alignment: inferring an alignment here would bury the aligner's parameters inside a tree.

## Request body

- object
  - `sequences` string, required: Aligned FASTA (gaps as "-"), or an array of {id, sequence}. All rows must be the same length. Max 200 sequences.
  - `sequenceType` 'auto' | 'dna' | 'protein': Which distance correction to use. Auto reads the alphabet: anything outside IUPAC nucleotide codes and gaps is taken as protein.
  - `bootstrapReplicates` integer: Felsenstein bootstrap replicates; 0 returns a tree with no support on it. 100 is the usual published figure.

## Response `200`

Tool ran successfully.

- SuccessResponse: Standard success envelope returned by every single-tool call.
  - `ok` unknown, required
  - `tool` string, required: The tool slug that ran.
  - `result` object, required: Tool-specific output object. Its shape depends on the tool — call `GET /{tool}` or see the docs for each tool's fields.
  - `gate` GateResult
    - `pass` boolean, required: True if and only if every hard check passed.
    - `checks` GateCheck[], required
      - `id` string, required
      - `label` string, required
      - `severity` 'hard' | 'soft', required
      - `pass` boolean, required
      - `message` string, required
      - `value` number
      - `threshold` string
    - `notChecked` string[], required: Honest list of what this gate does NOT verify.
  - `provenance` Provenance, required
    - `apiVersion` string, required
    - `tool` union, required: Tool slug, or an array of slugs (one per step) for a workflow.
      - string
      - string[]
    - `generatedAt` string, date-time, required: ISO 8601 timestamp of when the result was generated.

## Other responses

- `400`: Invalid argument or the tool could not run.
- `404`: Unknown tool.
- `429`: Rate limited (metered tools only). Body carries code `rate_limited` and retryable `true`; honor the Retry-After header.
- `503`: A metered tool is momentarily at capacity. The identical request should succeed after Retry-After; body carries code `upstream_unavailable`.

---

[API](https://skmtc.dev/seqbench/apis/seqbench-api.md) · [All operations](https://skmtc.dev/seqbench/apis/seqbench-api/llms.txt) · [OpenAPI document](https://skmtc.dev/seqbench/apis/seqbench-api/revisions/132575216865?raw)