Hi,
This is my input tree in newick format:
```
(VA13414_h:0.15657,(BK17487_h:0.09975,(VA2520_h:0.97287,VA15976_h:0.38081,(VA21335_h:0.19916,(TP1148_h:0.38815,VA24749_h:0.09725):1.29904):0.3596…
Hi there,
When I get more than one tree, I am able to find the consensus by running 'consense' in PHYLIP on all .newick trees. However, I am not able to merge or find the consensus for .gv output. …
Dear Xavier/Daniel,
I am having difficulty with running ClonalframeML. I have the appropriate input files e.g. a starting tree (.txt) in Newick format generated by phyml and an alignment of the seque…
> The product of λ or µ and the depth of the tree should not exceed one (i.e.,
> λ × t < 1 and µ × t < 1 must be true; where t is the time from tips to the
> root).
While verifying my results, I…
Hi,
I'm trying to create a phyloseq object that contains an OTU table and a phylogenetic tree downloaded from the SILVA database. I've followed the very helpful dada2 tutorial to create the OTU tab…
My tree has internal named nodes and leaves without names:
```
(,(,(,(,(,(,(,(,((,)temporary_t001,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,((,),(,(,(,(,(,(,(,((,),(,((,(,(,))Mol…
I was comparing your `from_linkage_matrix` function with my `linkage_to_newick` function:
```python
def from_linkage_matrix(cls, linkage_matrix, id_list):
"""Return tree from SciPy linkage matr…
@rneher, @tsibley, @jameshadfield, @emmahodcroft, @huddlej, @barneypotter24 ---
This issue is related to #133, but is definitely a separate decision.
I've been thinking about the use of Newick …