Open
Conversation
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
Owner
|
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 |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.