Maximum likelihood phylogenetic analysis (Sciuridae)

Knowledge graph centered on Maximum likelihood phylogenetic analysis (Sciuridae) with 30 nodes and 106 connections. Top connected: Marmota flaviventris, Apis mellifera, Marmota monax, chickens, All Chickens.

Method synopsis

Computational approach for constructing phylogenetic trees of viral protein sequences using maximum likelihood methods with various substitution models and statistical support assessment.

Synthesized from method descriptions across 1 paper 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 — Diverse cressdnaviruses and an anellovirus identified in the fecal samples of yellow-bellied marmots (2021), Virology. Implementations in other papers (listed below) may differ.

1. Phylogenetic analysis
   Sequences were assembled and annotated using Geneious v11.0.3. Maximum likelihood phylogenetic trees were constructed using PHYLML with various substitution models and branch support calculated using TreeGraph2
   Quantities: 31 viral genomes/molecules recoveredDuration: Not specifiedConditions: Computational analysis
   Equipment: Geneious v11.0.3, PHYLML, TreeGraph2

Typical Equipment

• Geneious v11.0.3
• PHYLML
• TreeGraph2

Output Measurements

• phylogenetic trees
• branch support values
• evolutionary relationships

Papers Using This Protocol (1)

Species Studied With This Protocol