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emmanuelparadis
/
ape
analysis of phylogenetics and evolution
http://ape-package.ird.fr/
GNU General Public License v2.0
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Obtaining the similarity matrix from rooted tree
#128
Ananya1006
closed
1 day ago
4
Fixed bug and added node label handling for discrete
#127
TGuillerme
opened
2 weeks ago
0
Unexpected value in dist.dna on sequences with gaps
#126
samcwiley
opened
1 month ago
1
Short question: how to interpret NAs in boot.phylo() bootstrapping?
#125
philoel
opened
1 month ago
1
Tree with a single tip but several nodes is not parsed correctly.
#124
kingaa
closed
1 month ago
2
Compilation failed during installation: `cc1plus: some warnings being treated as errors`.
#123
iago-lito
closed
2 months ago
2
is.ultrametric unexpected behavior
#122
pedrosenna
opened
2 months ago
4
Inheritance does not quite work with as.phylo
#121
lerouzic
closed
2 months ago
2
Add write.phyloXML() and corresponding tests
#120
fmarotta
opened
3 months ago
2
fix problems with x.lim and y.lim
#119
KlausVigo
closed
3 months ago
1
v5.8 drop.tip unexpected behavior
#118
colejensen
opened
3 months ago
3
fix spelling mistake
#117
KlausVigo
closed
4 months ago
2
axisPhylo() not extending all along the root edge
#116
emmanuelparadis
opened
4 months ago
0
Warn if node labels mismatched
#115
ms609
closed
5 months ago
3
read.tree() silently (but correctly) fails on malformed Newick file
#114
arcresu
closed
5 months ago
4
write.tree() may export duplicate internal node labels without notification
#113
stitam
closed
5 months ago
3
chronos() problems with convergence -- sometimes getting stuck entirely
#112
amizeranschi
closed
6 months ago
5
Some small improvements
#111
KlausVigo
closed
7 months ago
1
source/func call assist
#110
peterdunson
closed
6 months ago
2
help with source/func calls
#109
peterdunson
closed
7 months ago
1
Update as.phylo.formula.R
#108
peterdunson
closed
7 months ago
0
Confused about results of dist.nodes on BEAST output tree
#107
katherinermartin
closed
7 months ago
4
Adds node labels to ace output if available
#106
TGuillerme
closed
7 months ago
1
phymltest() producing the double amount of trees
#105
mickvv
opened
9 months ago
6
Newick tree with a single tip and more than one node not read correctly
#104
emmanuelparadis
closed
9 months ago
2
tree with root node
#103
KlausVigo
closed
4 months ago
5
Added a multiPhylo case to makeNodeLabel
#102
TGuillerme
closed
9 months ago
5
write.tree not using tree.names
#101
IanGBrennan
closed
11 months ago
2
allow del.gaps, del.rowgapsonly, del.colgapsonly to work on AAbin obj…
#100
KlausVigo
closed
11 months ago
3
biplot.pcoa() function produces different projections for the same variable when it is scaled.
#99
daroari
closed
8 months ago
3
Add color schemes to image.DNAbin and image.AAbin
#98
KlausVigo
closed
1 year ago
1
Error in nj(x) : cannot allocate memory block of size 134217728 Tb
#97
migueldiascosta
closed
1 year ago
7
Odd values in variance-covariance matrix
#96
kat3stewart
closed
1 year ago
2
No tip label for one of the tips
#95
lpipes
closed
1 year ago
6
wider support for zero-leaf trees
#94
emmanuelparadis
opened
1 year ago
0
Handle zero-leaf trees
#93
ms609
closed
1 year ago
2
Tree too large for cophenetic
#92
osidaksjdmw
closed
1 year ago
6
@KlausVigo I checked your PR (#90) which sounds great to me.
#91
KlausVigo
closed
8 months ago
1
improve keep.tip and drop.tip
#90
KlausVigo
closed
1 year ago
0
Cannot install ape in RStudio
#89
strawberry098
closed
1 year ago
1
Improvement
#88
KlausVigo
closed
1 year ago
3
new function: keep.as.tip
#87
HedvigS
closed
1 year ago
9
Cannot compute distance
#86
fullertonhe
closed
1 year ago
2
problem with nodelabels when frame="circle"
#85
Juanphg
closed
1 year ago
2
njs, bionj, and bionjs sometimes cause RStudio to abort when run on only 2 sequences
#84
FreekManders
closed
1 year ago
2
is.binary function with 0 branch lengths
#83
Lars-B
closed
1 year ago
3
corPhylo error - Error in Rd %*% R : non-conformable arguments
#82
MalharAtre
closed
1 year ago
5
model fit suspicious: gradients apparently non-finite
#81
xuechunxu
closed
1 year ago
2
`read.tree` seems to round branch lengths
#80
ajrominger
closed
1 year ago
3
Preserve Multiple Node Labels When Using drop.tip()
#79
simone-says
closed
1 year ago
2
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