# Comparing different models to BUSTED-PH ![](https://i.imgur.com/VdALNN5.png) ### PG-BSM * A Phenotype–Genotype Codon Model for Detecting Adaptive Evolution * Christopher T Jones, Noor Youssef, Edward Susko, Joseph P Bielawski * This is a sites model, focused more on nonadaptive shifting balance than adaptive evolution. Does this by finding an * Invertebrate cytochrome b- in mitochondria, highly conserved. Expected positive selection for transition from marine to other environments * terrestrial versus nonterrestrial, freshwater versus nonfreshwater, and intertidal versus nonintertidal * Two other alignments: phytochrome data (plants) and mammalian mtDNA (primates vs nonprimates) ### COEVOL * Paper: Genomic Signature of an Avian Lilliput Effect across the K-Pg Extinction * Jacob S. Berv, Daniel J. Field * Included a table full of trait values: mass_g, avg_maturity_days, gestation_incubation_days, clutch_size_per_year, birth_mass_g, growth_rate, longevity_yrs, metabolic_rate_w * Only mass_g was complete, other traits had lots of missing data * Took top 20% of mass values, put them in the foreground. Will have to compare this to the future model of busted-ph with continuous phenotypes ### RERconverge * Skipping this because of our collaboration, RERconverge will probably be in the paper anyway ### TraitRate[Prop] * Paper: What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda * Anieli G. Pereira, Mariana B. Grizante and Tiana Kohlsdor * Foreground species were defined as the ones characterized by the RAL morphotype the lumbar region corresponds to a posterior extension of the thorax exhibiting vertebrae with associated ribs in this region * HOXA10 gene ### Forward Genomics **This model does not use fastas, it uses a percent identity calculation. therefore i do not think it can be directly compared to busted-ph** * Vision-related convergent gene losses reveal SERPINE3’s unknown role in the eye ==> **the tree used from this paper made no sense.** * * Henrike Indrischek, Juliane Hammer, Anja Machate, Nikolai Hecker, Bogdan Kirilenko, Juliana Roscito, Stefan Hans, Caren Norden, Michael Brand, Michael Hiller * Authors of paper include some of coevolve’s original authors * Mostly relaxation of selection, not expected to see positive selection * Used UCSC data which we have had issues with. So I have a backup paper ### Phyloacc * Every paper I’ve looked at has used phyloacc for noncoding regions so I could not include this model. * Maybe it could be better compared to RERconverge ### Trait RELAX * A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution * Keren Halabi, Eli Levy Karin, Laurent Guéguen, Itay Mayrose * https://academic.oup.com/sysbio/article/70/3/608/6012374?login=false * Semenogelin II (SEMG2) in 24 primate species with respect to changes in the mating system * 68 genes from 50 species of γ-proteobacteria, of which 36 are free living and 14 are endosymbionts were examined.