emmanuelparadis / ape

analysis of phylogenetics and evolution

http://ape-package.ird.fr/

emmanuelparadis/ape Issues

v5.8 drop.tip unexpected behavior
Updated a month ago3
axisPhylo() not extending all along the root edge
Updated 3 months ago
tree with root node
Closed 3 months ago5
read.tree() silently (but correctly) fails on malformed Newick file
Closed 3 months ago4
write.tree() may export duplicate internal node labels without notification
Closed 3 months ago3
chronos() problems with convergence -- sometimes getting stuck entirely
Closed 4 months ago5
phymltest() producing the double amount of trees
Updated 5 months ago6
Confused about results of dist.nodes on BEAST output tree
Closed 5 months ago4
@KlausVigo I checked your PR (#90) which sounds great to me.
Closed 6 months ago1
Parallelization in dist.topo
Closed 6 months ago1
biplot.pcoa() function produces different projections for the same variable when it is scaled.
Closed 6 months ago3
Newick tree with a single tip and more than one node not read correctly
Closed 7 months ago1
write.tree not using tree.names
Closed 9 months ago2
Error in nj(x) : cannot allocate memory block of size 134217728 Tb
Closed 10 months ago7
corPhylo error - Error in Rd %*% R : non-conformable arguments
Closed 10 months ago5
No tip label for one of the tips
Closed a year ago6
possible bug in ace
Updated a year ago6
Odd values in variance-covariance matrix
Closed a year ago2
wider support for zero-leaf trees
Updated a year ago
Tree too large for cophenetic
Closed a year ago6
Cannot install ape in RStudio
Closed a year ago1
Improvement
Closed a year ago3
ape::drop.tip() unrooting tree
Closed 3 years ago14
Cannot compute distance
Closed a year ago2
is.binary function with 0 branch lengths
Closed a year ago3
problem with nodelabels when frame="circle"
Closed a year ago2
njs, bionj, and bionjs sometimes cause RStudio to abort when run on only 2 sequences
Closed a year ago2
model fit suspicious: gradients apparently non-finite
Closed a year ago2
`read.tree` seems to round branch lengths
Closed a year ago3
Preserve Multiple Node Labels When Using drop.tip()
Closed a year ago2
Issue in tree assignment
Closed a year ago
rtt function no longer handles NAs in dates
Closed a year ago5
segfault when reading in tree
Closed a year ago2
DESCRIPTION should list dependency R > 4.1
Closed a year ago2
Unable to install
Closed a year ago3
write.tree error
Closed 2 years ago25
can't read in tree
Closed 2 years ago3
ape::cophenetic.phylo() - Tree too big - any workarounds?
Closed 2 years ago2
Error: cannot use same sampling date for all the tips
Closed 2 years ago1
corBrownian error
Closed 2 years ago3
Potential bug when reading Mesquite formatting from nexus files
Closed 2 years ago1
version of keep.tip which considers internal nodes as well?
Closed 2 years ago18
Ladderize results C stack usage overflow
Closed 2 years ago6
wrong behaviour of is.monophyletic() with duplicated labels
Closed 2 years ago
read.tree() struggling with certain tip and node labels
Closed 2 years ago17
boot.phylo(): 'Error in 'bitsplits(phy)': INTEGER() can only be applied to a 'integer', not a 'double'
Closed 3 years ago5
can't write tree
Closed 3 years ago9
`c.multiPhylo` drops names
Closed 3 years ago2
`[<-.multiPhylo` does not support empty `[]`
Closed 3 years ago1
[<-.multiPhylo does not support empty []
Closed 3 years ago1