Maximum likelihood phylogenetic analysis

Knowledge graph centered on Maximum likelihood phylogenetic analysis with 60 nodes and 178 connections. Top connected: Bombus, Bombus terrestris, Bombus appositus, B. appositus, Bombus impatiens.

Method synopsis

Maximum likelihood phylogenetic analysis of full genome sequences using MUSCLE alignment and Tamura-Nei evolutionary model to determine relationships between outbreak isolates and assess overwintering versus new incursion.

Synthesized from method descriptions across 3 papers using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — Metagenome-assembled genomes for oligotrophic nitrifiers From a mountainous gravelbed floodplain (2025), Environmental Microbiology. Implementations in other papers (listed below) may differ.

1. Phylogenetic analysis
   Pangenomic and phylogenetic analyses were carried out using anvi'o (v8). Phylogenetic trees were constructed using IQ-TREE (v2.0.3) model finder -MFP to identify the best tree and 1000 bootstraps. Phylogenetic trees were visualized using FigTree (v1.4.4) and iTOL (v6). Alignments were carried out using Clustal Omega unless otherwise stated.
   Quantities: 1000 bootstrap replicates for phylogenetic treesDuration: Not specifiedConditions: Standard computational phylogenetic analysis conditions
   Equipment: anvi'o (v8), IQ-TREE (v2.0.3), FigTree (v1.4.4), iTOL (v6), Clustal Omega

Typical Equipment

• MegaX software
• MUSCLE alignment software
• FigTree v1.4.3

Output Measurements

• phylogenetic trees
• genetic similarity percentages
• evolutionary relationships

Papers Using This Protocol (3)

Species Studied With This Protocol