Maximum likelihood phylogenetic reconstruction (Limnephilidae)

Knowledge graph centered on Maximum likelihood phylogenetic reconstruction (Limnephilidae) with 18 nodes and 44 connections. Top connected: Lepidoptera, Trichoptera, Limnephilus externus, Asynarchus nigriculus, gene coalescence.

Method synopsis

Construction of phylogenetic trees from DNA sequence alignments using maximum likelihood method with HKY model and bootstrap analysis in PAUP*.

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 — Identifying PCR primers to facilitate molecular phylogenetics in Caddisflies (Trichoptera) (2015), Zoological Systematics. Implementations in other papers (listed below) may differ.

1. Process and analyze sequences
   Sequencing reactions were analyzed on an Applied Biosystems 3730xl automated sequencer. Sequences were edited in Sequencher 5.1 software before being aligned in CLUSTAL W. Sequence alignments were converted to NEXUS format and analyzed phylogenetically using maximum likelihood with HKY model in PAUP* 4.0b8/4.0a78.
   Quantities: Individual gene sequences and combined datasets analyzedDuration: Standard sequencing and analysis protocolsConditions: Laboratory sequencing and computational analysis conditions
   Equipment: Applied Biosystems 3730xl automated sequencer, Sequencher 5.1 software, CLUSTAL W, PAUP* 4.0b8/4.0a78

Typical Equipment

• PAUP* 4.0b8/4.0a78
• CLUSTAL W

Output Measurements

• phylogenetic trees
• bootstrap support values
• likelihood scores

Papers Using This Protocol (1)

Species Studied With This Protocol