treetime
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neherlab
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
I'm running this code and run into an index error: treetime --tree /Users/ouotodou/Desktop/treeee.nex --dates /Users/ouotodou/Desktop/sampled_metadata.csv --aln /Users/ouotodou/Desktop/sampled_sequences.fasta Attempting to parse dates... Using column 'strain' as name. This needs match the...
I got this error from refine that I struggled to debug: ``` ERROR: SequenceData: loading alignment failed... builds/masked.fasta ERROR from TreeTime: This error is most likely due to a problem...
Dear authors, Thanks a lot for providing the wonderful tools. I am faced with an error when I run: treetime --tree RAxML_bipartitions_ha_v3 --dates treetime_ha.csv --aln ha_v3_trim.fasta --time-marginal true --coalescent skyline...
Hi! Thank you for this very useful tool! My output does not contain confidence intervals even when I pass the command --confidence. below is what i am running on the...
Hi, Thanks a lot for creating treetime, looks like a very useful tool and I wanted to run this for reconstructing the ancestral sequences of my yeast genomes. I run:...
Also update `python_version>=3.7` for `extras_require` Logical follow up of https://github.com/neherlab/treetime/commit/92aad7c8a7423ae17bce97d9868101fb3c81d550
Hello, Do you consider adding binary alignement / models ? Thanks, Adrien
To be able to work with compressed alignments, which is useful e.g. for monkeypox, it would be nice if treetime could accept the string `/dev/stdin` for alignments. Right now, it...
Inspired by https://github.com/neherlab/treetime/issues/227 It could be helpful to output (multiple) root-to-tip-plots as they become available. Right now, it appears that multiple root-to-tip analyses are done, but only one plot is...
Hi, I am running treetime with `treetime --covariation --confidence --clock-filter 5 --tree --aln --dates ' ` on a selection of N1 subtype influenza viruses and it is returning the following:...
