PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of eukaryotic protein sequences.
*.treefile is the output tree from iqtree2
matrix_FULL.fa is the original matrix constructed at the end of the phylofisher workflow
However, here is what happens when I try to run it:
Traceback (most recent call last):
File "/opt/Anaconda3/envs/fisher_1.2.14/lib/python3.7/site-packages/ete3/coretype/tree.py", line 235, in __and__
first_match = next(self.iter_search_nodes(name=value))
StopIteration
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/Anaconda3/envs/fisher_1.2.14/bin/heterotachy.py", line 289, in <module>
series, size = get_branch_lens()
File "/opt/Anaconda3/envs/fisher_1.2.14/bin/heterotachy.py", line 93, in get_branch_lens
node2 = tree & taxon2
File "/opt/Anaconda3/envs/fisher_1.2.14/lib/python3.7/site-packages/ete3/coretype/tree.py", line 238, in __and__
raise TreeError("Node not found")
ete3.coretype.tree.TreeError: 'Node not found'
I have used the same data for the fast_site_removal.py script, and that one worked perfectly.
Any idea why this happens? Thanks
Hello, I have been trying to use the heterotachy.py script (phylofisher v1.2.14):
heterotachy.py -tr matrix_FULL.fa.treefile -m matrix_FULL.fa -s 2216*.treefile is the output tree from iqtree2 matrix_FULL.fa is the original matrix constructed at the end of the phylofisher workflow
However, here is what happens when I try to run it:
I have used the same data for the fast_site_removal.py script, and that one worked perfectly. Any idea why this happens? Thanks