Suhanaser patch 1 #5
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The distribution of GTR parameters from 49 empirical nucleotide datasets. The GTR parameters were estimated using IQ-TREE v1.7 All datasets are from Rob Lanfear's database (https://figshare.com/s/622e9e0a156e5233944b) The columns of the table are: * dataset: the name of the dataset (as it appears in the database) * partition: the name of the partition/locus (as it appears in the database) * sites: the number of sites in the partition * taxa: the number of taxa in the partition (does not include missing taxa from the original alignment) * A-C: substitution rate from A to C (and C to A) * A-G: substitution rate from A to G (and G to A) * A-T: substitution rate from A to T (and T to A) * C-G: substitution rate from C to G (and G to C) * C-T: substitution rate from C to T (and T to C) * G-T: substitution rate from G to T (and T to G) always equals to 1 * A: frequency of nucleotide A * C: frequency of nucleotide C * G: frequency of nucleotide G * T: frequency of nucleotide T * speed: the speed (scale) of the branch lengths * Gamma: the gamma distribution shape parameter for the rate heterogeneity across sites * invar: the proportion of invariant sites * type: type of the partition/loci: 1st, 2nd or 3rd codon position, rRNA, tRNA, UCE or other (intron, intergenic-spacer,.. etc.)
extract Q matrix, base frequency, %invariant sites and speed parameters from IQ-TREE file
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This is for the simulation project, right? If so, better to start a new repo for this. Keep this repo for the empirical SRH paper, so that it can be a good record of what we did in that paper. R |
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