Many research articles have removed the 3rd codon positions in PCGs and rRNA genes for the Phylogenetic tree construction.
The 3rd position of a codon, also called the wobble position can vary quite a lot. A nucleotide in this position can have many types of non Watson-Crick base pairing. In phylogenetics the removal or coding of this position is employed to reduce compositional heterogeneity, as it can drasticallly change the trees obtained.
Read about it over here:
Yang H, Li T, Dang K, Bu W. Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera). BMC Genomics. 2018;19(1):264. Published 2018 Apr 18. doi:10.1186/s12864-018-4650-9
Breinholt JW, Kawahara AY. Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data. Genome Biol Evol. 2013;5(11):2082-92. doi: 10.1093/gbe/evt157. PMID: 24148944; PMCID: PMC3845638.
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