[R-sig-phylo] HKY GTR distances
Dear Phylothusiasts, I need to compare multiple substitution models side-by-side (species clustering stuff by distances only). Unfortunately, I am not aware of an implementation of HKY and GTR distance computations using R. Maybe there is some Github code or something else that I have been missing? I do not want to build a phylogenetic tree. I can not use PAUP (>500 big fasta files). Any ideas are greatly appreciated. Best wishes, Andreas ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[R-sig-phylo] detect psbA-trnH inversions (and what to do with them) before phylogenetic reconstruction
Dear Phylothusiasts, what is the most reliable way (implemented in R) to detect inversions within psbA-trnH in large datasets (>1 seq)? What kind of treatment would you suggest before attempting a phylogenetic reconstruction (except exclusion)? Best wishes, Andreas @moderator: feel free to combine my two messages currently being held for moderation ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
