Authors
Felix Bast
Summary
This is a generic sequence analysis protocol suitable for plant and algal phylogeographic studies. Generated sequences from bidirectional Sanger sequencers are first assembled using Geneious. Sequence assembly is then trimmed and similarity search is conducted using BLASTn within Geneious. BLAST hits and other target taxa are selected and multiple sequence alignment is constructed. The alignment is then refined by checking using eye and exported as .fasta. Using MEGA, best-fitting nucleic acid substitution models will be calculated in MLModelTest. Model with lowest BIC score is selected and used for further phylogenetic analysis using MEGA or Geneious, which include distance matrix construction, phylogeny reconstruction using ML and BI.Further details
The protocol was published on Protocol Exchange on 11 July 2013. To see the entire protocol, click on the source link.Advertisement
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