treetime
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neherlab
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
Is it possible to know more specifically on which branch/node this error occurs? That could be useful for debugging the tree! _Originally posted by @corneliusroemer in https://github.com/neherlab/treetime/pull/202#discussion_r943333323_
Hallo TT team, I'm getting this error running treetime locally on my Mac and on the server (CentOS 7). treetime clock --tree new_tree3.nwk --dates dates.csv --aln nextalign.aligned.new_tree3.fasta --reroot "oldest" 0.00...
Thank you for Treetime. I am using it to identify and remove excessively divergent (and probably erroneous) sequences from a large dataset of viral sequences. When TT rejects a sequence...
Hi I have created a tree using RaxML of a bacterial dataset which has ~4000 tips. For downstream analysis I need this to be ultrametric, but am struggling to find...
Going through the source code I realised that 2 each of the 4 possible ancestral reconstruction methods are synonyms. Note to future self before I forget: This could be explained...
Many thanks for developing this tool! I am currently receiving the following error message: `ValueError: zero-size array to reduction operation minimum which has no identity` I looked at the related...
Hi all, Just wondering if it would be possible to add the branch_lengths table that is generated in the Augur/Nextstrain version of Tree Time as an additional output in the...
Dear all, I'm trying you use TreeTime for the first time. I have tried the mugration model on a tree built with few sequences establishing two states only (two countries)....
In the TreeTime .nexus output I get a huge negative branch len followed by another large on for the corresponding leaves: ``` ... ((7ab5cd3e-524b-4f3e-9951-04d783bcef78:28113.25709,5abe8078-fdb6-4e90-9075-314bc4238f48:28113.15326)NODE_0000024:-28112.91947,(dd518f5c-d48a-464d-bff3-4becb51ae5d5:0.00000,0e2e43b1-45fc-4a32-b584-d4db7b91e86b:0.00000) ... ``` Is this a bug...
