What alignment and trimming tools are included in the workflow?

The workflow supports MAFFT for alignment and offers multiple trimming options including Aliscore/ALICUT, trimAl, BMGE, and ClipKit.

Which job schedulers are supported by this skill?

The skill supports SLURM, PBS/Torque, and local machine execution using GNU parallel, providing specific templates for each environment.

Can I use genomes from both local storage and NCBI?

Yes, the skill handles mixed inputs and provides scripts to query, download, and rename NCBI assemblies alongside your local files.

How does the skill handle software installation?

It generates a unified environment setup script that uses Conda or Mamba to install all necessary bioinformatics tools and dependencies.

Does it help with selecting evolutionary models?

Yes, it uses a systematic approach to recommend amino acid substitution models for IQ-TREE based on your dataset's taxonomic breadth and sequence characteristics.

Phylogenomics Workflow Generator

Name: Phylogenomics Workflow Generator
Author: brunoasm

bybrunoasm

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Data Science & ML

Automates the generation of scheduler-aware phylogenomic workflows from genome assemblies using single-copy orthologs.

About

This skill provides specialized bioinformatics expertise for building comprehensive phylogenetic trees from genomic data. It manages the entire pipeline—from querying and downloading NCBI assemblies to performing BUSCO/compleasm analysis, ortholog extraction, alignment, and maximum likelihood tree inference. It is specifically designed to generate optimized scripts for SLURM, PBS/Torque, and local computing environments, ensuring reproducible and efficient phylogenomic analyses.

Key Features

Advanced alignment trimming options including Aliscore and ALICUT
Intelligent substitution model recommendation for IQ-TREE
Hybrid input handling for local genome files and NCBI accessions
3 GitHub stars
Automated workflow generation for SLURM, PBS, and local machines
Integrated quality control and single-copy ortholog extraction scripts

Use Cases

Generating a species-level phylogeny from a collection of newly sequenced genome assemblies
Scaling ortholog identification and alignment across high-performance computing clusters
Systematically querying and downloading public genomic datasets for comparative genomics

About

Key Features

Advanced alignment trimming options including Aliscore and ALICUT
Intelligent substitution model recommendation for IQ-TREE
Hybrid input handling for local genome files and NCBI accessions
3 GitHub stars
Automated workflow generation for SLURM, PBS, and local machines
Integrated quality control and single-copy ortholog extraction scripts

Use Cases

Generating a species-level phylogeny from a collection of newly sequenced genome assemblies
Scaling ortholog identification and alignment across high-performance computing clusters
Systematically querying and downloading public genomic datasets for comparative genomics