University of Pretoria
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Phylogenetic analysis of Penicillium, used to re-identify Penicillium genomes available in the National Center for Biotechnology Information (NCBI)

posted on 2023-09-05, 11:05 authored by Cobus VisagieCobus Visagie

Alignment files and output Trees from phylogenetic analyses.

Data sets were aligned in MAFFT v. 7.490 (Katoh & Standley 2013) with the G-INS-I option selected, with alignments manually trimmed, adjusted and concatenated in Geneious where needed. The most appropriate partition schemes and substitution models were selected based on Bayesian information criterion using a greedy strategy implemented in PartitionFinder v. 2.1 (Lanfear et al. 2017), allowing gene regions, introns, exons and codon positions to be independent datasets. Phylogenies were calculated using both Maximum Likelihood (ML) and Bayesian tree Inference (BI). ML was performed in IQtree v. 2.2.0 (Minh et al. 2020) with support in nodes calculated using a bootstrap analysis of 1000 replicates. BI was performed in MrBayes v. 3.2.7 (Ronquist et al. 2012), with three sets of four chains (1 cold and three heated) and was stopped at an average standard deviation for split frequencies of 0.01 using the "stoprule".



Forestry and Agricultural Biotechnology Institute

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