Simulate an alignment from a known tree
simulate_alignmentRead-onlyIdempotent
Generate synthetic sequence alignments with a known true tree to test and validate phylogenetic inference methods.
Instructions
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.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| seed | No | ||
| model | No | JC | |
| length | No | ||
| newick | Yes |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| seed | Yes | ||
| fasta | Yes | ||
| model | Yes | ||
| warnings | Yes | ||
| alignment | Yes | ||
| true_newick | Yes |