---
name: phylogenetics-tree-builder-7f53d96efb3b
description: Phylogenetic analysis skill for constructing evolutionary trees and assessing relationships
allowed-tools:
  - Read
  - Write
  - Glob
  - Grep
  - Edit
  - WebFetch
  - WebSearch
  - Bash
metadata:
  version: "1.0"
  category: bioinformatics
  tags:
    - sequence-analysis
    - phylogenetics
    - evolution
    - trees
graph:
  domains: [domain:bioinformatics]
  specializations: [specialization:biomedical-informatics]
  skillAreas: [skill-area:graph-algorithms, skill-area:statistical-analysis, skill-area:mathematical-reasoning]
  workflows: [workflow:experiment-design]
  roles: [role:research-scientist, role:computational-scientist]
---

# Phylogenetics Tree Builder Skill

## Purpose
Enable phylogenetic analysis for constructing evolutionary trees, performing multiple sequence alignments, and assessing phylogenetic relationships.

## Capabilities
- Multiple sequence alignment (MUSCLE, MAFFT)
- Maximum likelihood tree construction
- Bayesian phylogenetic inference
- Bootstrap support calculation
- Tree visualization and annotation
- Molecular clock analysis

## Usage Guidelines
- Align sequences before tree construction
- Select appropriate substitution models
- Calculate bootstrap support for branch confidence
- Visualize trees with meaningful annotations
- Consider molecular clock constraints when appropriate
- Document methodology and parameters

## Dependencies
- RAxML-NG
- IQ-TREE
- MrBayes
- MAFFT
- MUSCLE
- FigTree

## Process Integration
- 16S rRNA Microbiome Analysis (16s-microbiome-analysis)
- Shotgun Metagenomics Pipeline (shotgun-metagenomics)
- Whole Genome Sequencing Pipeline (wgs-analysis-pipeline)


---
Source attribution: a5c-ai
Original project: https://github.com/a5c-ai/babysitter
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Mega AI Hub.

## Upstream license notice

MIT License

Copyright (c) 2026 Gabriel Moreira

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Mega AI Hub resource metadata

Creator / publisher: a5c-ai
Original project: https://github.com/a5c-ai/babysitter
Attribution basis: Upstream repository explicitly recorded in package mirror path

Fields of work: Data & Analytics, Education & Research
Roles: Data Scientist, Researcher
Specialties: API
Tools: Figtree, Iq Tree, Mafft, Muscle, Mrbayes, Raxml Ng
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: 0d26fd4a3c0a59c5727086fc2c60624364fbfef24a8bc3dca950b842cbb1bacb