maximum likelihood phylogeny

Knowledge graph centered on maximum likelihood phylogeny with 71 nodes and 166 connections. Top connected: Crested Butte, Pekania pennanti, Salix lucida subsp. lasiandra, Lepidoptera, Bacteria.

Method synopsis

Construction of phylogenetic trees using concatenated ribosomal protein genes to determine evolutionary relationships. Uses IQ-TREE with maximum likelihood approach and bootstrap support.

Synthesized from method descriptions across 4 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. Metagenome assembly and binning
   Assemblies and co-assemblies were made using MEGAHIT (v1.3.3) and binned using contigs > 2000 nt and > 2500 nt, respectively, using MetaBAT2 (v2.12.1), MaxBin 2.0 (v2.2.6), and CONCOCT (v1.0.0) with multiple fastq files grouped by surface (50cm depth), middle depth (70-110 cm), and anoxic depths (130-150 cm). Bins were consolidated and filtered using metawrap bin_refinement to be above > 50% completeness and have < 10% contamination as calculated via CheckM (v1.1.3).
   Quantities: Contigs > 2000 nt for assemblies, > 2500 nt for co-assemblies, >50% completeness and <10% contamination thresholdsDuration: Not specifiedConditions: Standard computational processing conditions
   Equipment: MEGAHIT (v1.3.3), MetaBAT2 (v2.12.1), MaxBin 2.0 (v2.2.6), CONCOCT (v1.0.0), CheckM (v1.1.3)

Typical Equipment

• IQ-TREE software

Output Measurements

• phylogenetic trees
• bootstrap support values

Papers Using This Protocol (4)

Species Studied With This Protocol

Places Where Used