phylogenetics

To build a phylogenetic tree from a FASTA file, you need multiple sequence alignment followed by tree inference. This pipeline automates the process using MAFFT for alignment and IQ-TREE 2 for maximum-likelihood tree construction.

For large microbial datasets, FastTree provides a fast alternative for inferring evolutionary trees. This pipeline supports FastTree specifically for large-scale phylogenetic analysis where standard maximum-likelihood methods would be too computationally expensive.

Yes, you can visualize phylogenetic trees in Python using ETE3. The pipeline utilizes ETE3 to generate tree visualizations and compute basic tree statistics directly within a Python environment.

IQ-TREE 2 supports automatic model selection for maximum-likelihood tree inference, which is applicable to molecular clock studies. This pipeline leverages IQ-TREE 2 to infer branching patterns and divergence times for evolutionary analysis.

To perform multiple sequence alignment for viral phylodynamics, MAFFT is used to align nucleotide or protein sequences. This pipeline applies MAFFT to prepare sequence data for downstream evolutionary tree inference.