Is automated model selection included?

Yes, it utilizes IQ-TREE 2's ModelFinder (TEST) to automatically identify the best-fit substitution model for your specific sequence data.

Can I use this for both DNA and protein sequences?

Yes, the workflows include specific logic and model selection guides for both nucleotide (nt) and amino acid (aa) sequences.

Which phylogenetic tools are supported by this skill?

The skill supports MAFFT for sequence alignment, IQ-TREE 2 for maximum likelihood trees, FastTree for large-scale datasets, and ETE3 for tree visualization and manipulation.

How does this skill handle large genomic datasets?

For datasets exceeding 1,000 sequences, the skill provides optimized FastTree configurations to ensure rapid tree inference without excessive computational overhead.

Phylogenetics & Evolutionary Analysis

Name: Phylogenetics & Evolutionary Analysis
Author: lingxling

bylingxling

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データサイエンスとML

Reconstructs evolutionary histories by building, analyzing, and visualizing phylogenetic trees from biological sequences.

This skill provides a comprehensive bioinformatics pipeline for researchers and developers to analyze the evolutionary relationships between genes, proteins, and genomes. It streamlines the transition from raw FASTA sequences to publication-quality trees by integrating industry-standard tools like MAFFT for alignment, IQ-TREE 2 for maximum likelihood inference, and FastTree for high-speed processing of large datasets. Whether you are tracking viral outbreaks, studying microbial genomics, or performing protein family analysis, this skill automates the complex workflows of model selection, bootstrapping, and tree visualization.

主な機能

0139 GitHub stars

02High-accuracy Maximum Likelihood tree inference with IQ-TREE 2

03Automated Multiple Sequence Alignment (MSA) using MAFFT

04Fast approximate ML tree generation for large datasets with FastTree

05Integrated support for both nucleotide and amino acid sequence models

06Programmable tree manipulation and visualization via the ETE3 Python library

ユースケース

01Identifying horizontal gene transfer and discordant species-gene trees

02Inferring ancestral protein sequences for evolutionary functional studies

03Tracing viral phylodynamics to track outbreak spread and transmission dates

主な機能

0139 GitHub stars

02High-accuracy Maximum Likelihood tree inference with IQ-TREE 2

03Automated Multiple Sequence Alignment (MSA) using MAFFT

04Fast approximate ML tree generation for large datasets with FastTree

05Integrated support for both nucleotide and amino acid sequence models

06Programmable tree manipulation and visualization via the ETE3 Python library

ユースケース

01Identifying horizontal gene transfer and discordant species-gene trees

02Inferring ancestral protein sequences for evolutionary functional studies

03Tracing viral phylodynamics to track outbreak spread and transmission dates