text: user9651: I am performing amino acid analysis but require assistance in the underlying amino acid substitution model, i.e. the predetermined rate/frequency of amino acid mutations which are used for example in constructing phylogenetics trees using maximum likelihood or Bayesian methods.
  There are numerous matrices of probabilities for every combination of amino acids (something like BLOSUM or PAM matrices and I am wondering within the large number of models which the most appropriate. I am aware there is no 'universal' matrix.
  I want to use the matrix to check the probability of amino acid substitution in sequence on a pairwise basis.
  For example, I'm not sure whether the BLOSUM or PAM matrix will be useful to me.
  [EXTRA] If all diagonal values in such a matrix would be equal to 1 that would be helpful.
  
  user3848: The LG model is here:
  0.425093 
  0.276818 0.751878 
  0.395144 0.123954 5.076149 
  2.489084 0.534551 0.528768 0.062556 
  0.969894 2.807908 1.695752 0.523386 0.084808 
  1.038545 0.363970 0.541712 5.243870 0.003499 4.128591 
  2.066040 0.390192 1.437645 0.844926 0.569265 0.267959 0.348847 
  0.358858 2.426601 4.509238 0.927114 0.640543 4.813505 0.423881 0.311484 
  0.149830 0.126991 0.191503 0.010690 0.320627 0.072854 0.044265 0.008705 0.108882 
  0.395337 0.301848 0.068427 0.015076 0.594007 0.582457 0.069673 0.044261 0.366317 4.145067 
  0.536518 6.326067 2.145078 0.282959 0.013266 3.234294 1.807177 0.296636 0.697264 0.159069 0.137500 
  1.124035 0.484133 0.371004 0.025548 0.893680 1.672569 0.173735 0.139538 0.442472 4.273607 6.312358 0.656604 
  0.253701 0.052722 0.089525 0.017416 1.105251 0.035855 0.018811 0.089586 0.682139 1.112727 2.592692 0.023918 1.798853 
  1.177651 0.332533 0.161787 0.394456 0.075382 0.624294 0.419409 0.196961 0.508851 0.078281 0.249060 0.390322 0.099849 0.094464 
  4.727182 0.858151 4.008358 1.240275 2.784478 1.223828 0.611973 1.739990 0.990012 0.064105 0.182287 0.748683 0.346960 0.361819 1.338132 
  2.139501 0.578987 2.000679 0.425860 1.143480 1.080136 0.604545 0.129836 0.584262 1.033739 0.302936 1.136863 2.020366 0.165001 0.571468 6.472279 
  0.180717 0.593607 0.045376 0.029890 0.670128 0.236199 0.077852 0.268491 0.597054 0.111660 0.619632 0.049906 0.696175 2.457121 0.095131 0.248862 0.140825 
  0.218959 0.314440 0.612025 0.135107 1.165532 0.257336 0.120037 0.054679 5.306834 0.232523 0.299648 0.131932 0.481306 7.803902 0.089613 0.400547 0.245841 3.151815 
  2.547870 0.170887 0.083688 0.037967 1.959291 0.210332 0.245034 0.076701 0.119013 10.649107 1.702745 0.185202 1.898718 0.654683 0.296501 0.098369 2.188158 0.189510 0.249313 
  
  Where the amino acid frequencies are:
  0.079066 0.055941 0.041977 0.053052 0.012937 0.040767 0.071586 0.057337 0.022355 0.062157 0.099081 0.064600 0.022951 0.042302 0.044040 0.061197 0.053287 0.012066 0.034155 0.069147
  Amino acid order (matrix and frequencies)
  A R N D C Q E G H I L K M F P S T W Y V
  Reference
  Le S.Q., Gascuel O. Molecular Biology and Evolution. 2008 25(7):1307-20.
  
original_text: 9651: <p>I am performing amino acid analysis but require assistance in the underlying amino acid substitution model, i.e. the predetermined rate/frequency of amino acid mutations which are used for example in constructing phylogenetics trees using maximum likelihood or Bayesian methods.</p>
  <p>There are numerous matrices of probabilities for every combination of amino acids (something like <a href="https://en.wikipedia.org/wiki/Substitution_matrix" rel="nofollow noreferrer"><em>BLOSUM</em> or <em>PAM</em></a> matrices and I am wondering within the large number of models which the most appropriate. I am aware there is no 'universal' matrix.</p>
  <p>I want to use the matrix to check the probability of amino acid substitution in sequence on a pairwise basis.</p>
  <p>For example, I'm not sure whether the BLOSUM or PAM matrix will be useful to me.</p>
  <p>[<strong>EXTRA</strong>] If all diagonal values in such a matrix would be equal to <code>1</code> that would be helpful.</p>
   3848: <p>The LG model is here:</p>
  <pre><code>0.425093 
  0.276818 0.751878 
  0.395144 0.123954 5.076149 
  2.489084 0.534551 0.528768 0.062556 
  0.969894 2.807908 1.695752 0.523386 0.084808 
  1.038545 0.363970 0.541712 5.243870 0.003499 4.128591 
  2.066040 0.390192 1.437645 0.844926 0.569265 0.267959 0.348847 
  0.358858 2.426601 4.509238 0.927114 0.640543 4.813505 0.423881 0.311484 
  0.149830 0.126991 0.191503 0.010690 0.320627 0.072854 0.044265 0.008705 0.108882 
  0.395337 0.301848 0.068427 0.015076 0.594007 0.582457 0.069673 0.044261 0.366317 4.145067 
  0.536518 6.326067 2.145078 0.282959 0.013266 3.234294 1.807177 0.296636 0.697264 0.159069 0.137500 
  1.124035 0.484133 0.371004 0.025548 0.893680 1.672569 0.173735 0.139538 0.442472 4.273607 6.312358 0.656604 
  0.253701 0.052722 0.089525 0.017416 1.105251 0.035855 0.018811 0.089586 0.682139 1.112727 2.592692 0.023918 1.798853 
  1.177651 0.332533 0.161787 0.394456 0.075382 0.624294 0.419409 0.196961 0.508851 0.078281 0.249060 0.390322 0.099849 0.094464 
  4.727182 0.858151 4.008358 1.240275 2.784478 1.223828 0.611973 1.739990 0.990012 0.064105 0.182287 0.748683 0.346960 0.361819 1.338132 
  2.139501 0.578987 2.000679 0.425860 1.143480 1.080136 0.604545 0.129836 0.584262 1.033739 0.302936 1.136863 2.020366 0.165001 0.571468 6.472279 
  0.180717 0.593607 0.045376 0.029890 0.670128 0.236199 0.077852 0.268491 0.597054 0.111660 0.619632 0.049906 0.696175 2.457121 0.095131 0.248862 0.140825 
  0.218959 0.314440 0.612025 0.135107 1.165532 0.257336 0.120037 0.054679 5.306834 0.232523 0.299648 0.131932 0.481306 7.803902 0.089613 0.400547 0.245841 3.151815 
  2.547870 0.170887 0.083688 0.037967 1.959291 0.210332 0.245034 0.076701 0.119013 10.649107 1.702745 0.185202 1.898718 0.654683 0.296501 0.098369 2.188158 0.189510 0.249313 
  </code></pre>
  <p>Where the amino acid frequencies are:</p>
  <p>0.079066 0.055941 0.041977 0.053052 0.012937 0.040767 0.071586 0.057337 0.022355 0.062157 0.099081 0.064600 0.022951 0.042302 0.044040 0.061197 0.053287 0.012066 0.034155 0.069147</p>
  <p><strong>Amino acid order</strong> (matrix and frequencies)</p>
  <p>A R N D C Q E G H I L K M F P S T W Y V</p>
  <p><strong>Reference</strong>
  Le S.Q., Gascuel O. Molecular Biology and Evolution. 2008 25(7):1307-20.</p>
  