Build phylogenetic trees from sequence alignments using MAFFT, IQ-TREE 2, and ETE3.
npx skills add https://github.com/shushuzn/Rairos --skill phylogenetics-shushuzn
Please help me install this Agent Skill. Skill: phylogenetics Source: https://github.com/shushuzn/Rairos/tree/main/skills/phylogenetics Command: npx skills add https://github.com/shushuzn/Rairos --skill phylogenetics-shushuzn
This Skill helps you reconstruct phylogenetic relationships by turning raw nucleotide or protein sequence data into multiple sequence alignments, maximum-likelihood trees, and visualizations you can interpret.
Run the provided phylogenetic analysis script on your FASTA file by invoking: python phylogenetic_analysis.py sequences.fasta --type nt --threads 4.
High-intent search queries and answers about installing and using this skill.
To build a phylogenetic tree from a FASTA file, run the phylogenetic analysis script with your sequences, specifying the sequence type and threads. The workflow uses MAFFT for alignment and IQ-TREE 2 for maximum likelihood tree inference.
For large datasets, FastTree produces fast approximate phylogenetic trees when full maximum likelihood runs become too computationally expensive. This provides a faster alternative to IQ-TREE 2 for large-scale sequence analysis.
You can visualize and root Newick tree outputs using ETE3, which loads the tree files, applies midpoint or outgroup rooting, computes basic tree statistics, and renders publication-ready figures.
Yes, IQ-TREE 2 supports microbial genomics by inferring best-fit evolutionary trees with built-in model selection and ultrafast bootstrap support to validate phylogenetic relationships.
Yes, MAFFT is required to build multiple sequence alignments from raw nucleotide or protein sequence data before passing the aligned sequences to IQ-TREE 2 or FastTree for tree inference.
Yes, the IQ-TREE 2 inference step supports optional molecular clock dating workflows by providing date inputs alongside your sequence alignment to estimate evolutionary timelines.
JosephWoodallInfer evolutionary relationships from nucleotide or protein sequences using MAFFT, IQ-TREE 2, and ETE3.
Estrella-231Infer maximum-likelihood phylogenetic trees from unaligned FASTA sequences.
jasrajtulsiBuild rooted phylogenetic trees from biological sequences using MAFFT, IQ-TREE 2, and ETE3.
biomaps-infraBuild and analyze phylogenetic trees using MAFFT, IQ-TREE 2, and FastTree.
