Inference phylogenetically placing Phytophthora cyperi using mitochondrial cox1 sequences
Description
Relevant files used in the phylogenetic inference featured in Bourret et al. (2024) (under review): First detection of the obligate biotroph Phytophthora cyperi causing a disease on yellow nutsedge in the United States, and establishment of molecular barcoding sequences for the species (PhytoFrontiers). The files consist of a list of sequence accessions, the mitochondrial cox1 alignment, and output files from IQ-TREE 2 (Partition and model-finding + maximum likelihood phylogenetic inference), PartitionFinder2 (Partition and model-finding for Bayesian analysis) and MrBayes 3.2.6 (Bayesian phylogenetic inference)
Files
Steps to reproduce
The sequence accessions that are the basis of this dataset are all publicly available from NCBI and listed in sequence_accessions.xlsx. To reproduce the dataset, the sequences would be downloaded and aligned with a multi-sequence alignment program (MAFFT L-ins-i was used in this case, but the nature of the dataset suggests any aligner will produce an identical alignment), then trimmed, producing a file similar or identical to the alignment file (cox1.95x1344.phy). To reproduce the IQ-TREE analysis, the exact command used can be found in the .log file. The configuration file used for PartitionFinder is included, and the MrBayes section of that output was used to configure MrBayes.