nclark-lab / RERconverge

Analysis of convergence between organismal traits and DNA/protein sequences

nclark-lab/RERconverge Issues

How to get the RERs of ancestral nodes?
Updated a month ago3
fastwilcoxGMTall with Goterms instead of pathways
Updated a month ago2
tree discordance and multiple-copy genes
Updated 3 months ago9
Permulations using `tree2Paths()`?
Updated 3 months ago2
question about getAllResiduals
Updated 3 months ago
How to conduct tests for Phylogenetic Permutations of Binary Phenotypes with two ancestral branches?
Updated 3 months ago
mamRERw result is NA
Updated 3 months ago6
A large number of Duplicate columns and NA columns after running getAllResiduals
Closed 4 months ago1
can i provide a neutral tree with branch length as RERconverge master tree
Updated 4 months ago2
RERconverge Install Error (M2 Mac OS Ventura 13.6.7)
Closed 4 months ago1
whether RERconverge has to be used for converge ?
Updated 5 months ago2
Ask a stupid question, where can i find the scripts in the NoncodingRegionWorkflow file
Updated 6 months ago2
Number of input species and explanation of output
Closed 7 months ago4
How to optimize parameters based on my current results?
Updated 7 months ago2
Discordant gene trees
Closed 8 months ago
not enough genes with all species present: master tree has no edge.lengths
Updated 8 months ago2
Trouble installing on Intel Core Mac
Updated 10 months ago1
Trouble installing RERconverge on M1 mac
Updated a year ago3
Unable to load RERconverge on M1 Mac
Updated a year ago2
Error when trying to read in treefile
Closed a year ago8
Error: Mat::elem(): index out of bounds
Updated 2 years ago2
binarize option not working correctly in the tree2Paths function
Updated 2 years ago1
Differences between clade-based correlation and non-clade based correlations?
Updated 2 years ago1
Bioconda package
Closed 2 years ago1
'masterTree' not found in SSM permulations
Closed 2 years ago
Update getPermsBinary with earlier non-numeric check
Updated 2 years ago2
Different rho and p-values for the same gene in the table and figure
Closed 2 years ago6
Error when running getAllResiduals (incorrect pseudorooting)
Updated 2 years ago2
Cannot Install RERconverge
Closed 3 years ago7
Erro when using estimatePhangornTreeAll
Updated 3 years ago5
long branch length due to missing
Closed 3 years ago3
Can RERconverge handle gene trees with duplicates?
Updated 3 years ago2
readTrees() and subsequent getAllResiduals errors
Updated 3 years ago3
Labels in RERplots
Updated 3 years ago
Pseudorooting of Genetrees
Updated 3 years ago
Trouble calculating RER by getAllResiduals, all NA generated
Updated 4 years ago11
readTrees() and subsequent getAllResiduals errors
Closed 5 years ago7
Unable to Install Program
Updated 4 years ago13
Issues installing RERconverge on R 4.0 (Mac OS Catalina 10.15.5)
Closed 4 years ago4
Output of fastwilcoxGMTAll
Closed 4 years ago1
Gene tree input other than PAML
Closed 4 years ago5
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
Closed 4 years ago11
Issues installing from binary on MacOS Mojave 10.14.6
Closed 5 years ago6
Does the paralog genes from the same gene tree affect the output?
Closed 5 years ago2
correlateWithBinary Error in lm.wfit 0 (non-NA) cases
Updated 5 years ago2
idea for improved handling of discordant tree topologies in readTrees
Updated 5 years ago
Trouble calculating RER by getAllResiduals, NaN generated when read trees
Closed 5 years ago2
data directory does not contain trees
Closed 5 years ago10
Releases
Closed 6 years ago2
Separate parameters for clade, weighting, and allowed transitions in foreground2Tree
Closed 6 years ago