[R-sig-phylo] ape::muscle doesn't work with Muscle5

Hello, ape::muscle() works well with MUSCLE 3.8.31 from , but not with v. 5.1 (released recently). I run it as 'ape::muscle(x=gunnera.dna, exec="muscle", quiet=FALSE, original.ordering=TRUE)' and I get

[R-sig-phylo] PGLS incorporating weights and estimate of effect size

Hello, Co-authors and I want to run PGLS analyses including weights based on the number of individuals from which the dependent variable is estimated, as an estimate of the confidence of the species mean value. We’ve run models in gls with the necessary control for phylogenetic