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protmodels

General repository for models of protein evolution developed by the Braun research group

Programs used to compare matrices:

  1. normalize_vectors.pl
  2. calcEucl.pl

To conduct a comparison of R matrices the matrices are written as a tab delimited file with vectors of 190 values, each preceded by the model name. Then normalize_vectors.pl is used to normalize these vectors to sum to one and calcEucl.pl is used to calculate distances among those vectors.

GKB mt transmembrane

Models from: Gordon, E.L.; Kimball, R.T.; Braun, E.L. Protein structure, models of sequence evolution, and data type effects in phylogenetic analyses of mitochondrial data: A case study in birds. Diversity 2021, 13, 555. https://doi.org/10.3390/d13110555

Five files, plus a more detailed README:

  1. JTTtm.paml.txt
  2. bird_mtExM.paml.txt
  3. bird_mtTM.paml.txt
  4. bird_mtMIX_JTTtm.nex
  5. matrix_comparisons_bird_JTTtm.xlsx

Three paml format rate matrices, a nexus format mixture model (two components, one for transmembrane sites, and extramembrane sites), and an Excel spreadsheet with calculations for the JTTtm model (derived from Jones et al. 1994 using the Kosiol and Goldman 2005 DCMut method)

Additional references:

Jones, D.T.; Taylor, W.R.; Thornton, J.M. A mutation data matrix for transmembrane proteins. FEBS Lett. 1994, 339, 269–275, doi:10.1016/0014-5793(94)80429-x.

Kosiol, C.; Goldman, N. Different versions of the Dayhoff rate matrix. Mol. Biol. Evol. 2005, 22, 193–199, doi:10.1093/molbev/msi005.

Scolaro Braun 2021 models

Models from: Scolaro, G.E.; Braun, E.L. The structure of evolutionary model space for proteins across the tree of life. Submitted

Models from Scolaro & Braun were trained on alignments from various bacterial and archaeal clades. Those with the prefix "ribo" were trained on ribosomal proteins and those with no prefix were trained on arbitrarily chosen proteins. Models from previous publications that were considered by Scolaro & Braun are also included in the folder.