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sdellicour / sars_cov_2_pipeline

Analytical pipeline developed and applied for the study “A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages” (Dellicour et al. 2021, Mol. Biol. Evol.)
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Beast 1.10.4 error :NEWICK tree is not fully bifurcated #1

Open Sikandar37 opened 12 months ago

Sikandar37 commented 12 months ago

Dear Simon, I am doing Discrete phylogeographic analysis for a dataset of 2600 influenza sequences following your paper. A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages ](https://academic.oup.com/mbe/article/38/4/1608/5952687). I used IQTree to generate a maximum likelihood tree and after removing outlier sequences, the time calibrated Tree was constructed in nexus format using TreeTime . after loading the tree into BEAST V.10.4 I am getting an error that tree file is not fully bifurcated but the same tree is working well for Beast V.2.7.4 . I am wondering how did you import the tree generated by TreeTime into beast V.10.4. did you try additional step to make the tree fully bifurcated in this paper. . I am looking forward to hear from you Thank you

sdellicour commented 12 months ago

Hi Sikandar,

for that study we ran TreeTime such that it resolves the polytomies (https://treetime.readthedocs.io/en/latest/), which is indeed a requirement to use the time-calibrated as a fixed empirical tree topology in BEAST 1.10

I hope this helps, Best,

Simon

Sikandar37 commented 12 months ago

Dear simon, Thank you very much for your quick and useful information. Previously i was using the script treetime --tree tree_file --aln alignment --dates dates.tsv and i was getting error while importing the tree . After following your suggestion i changed the script and it worked well treetime clock --tree tree6.newick --dates metadata.csv --aln sequences6.fas --clock-filter 4 i got output tree in newick format. later on i changed into nexus using Ape package in R. and tree was successfully imported into the beauti. I have some questions . While setting the time caliberated tree as starting tree. What did you choose as substitution model/clock model/tree prior model/ I have read the supplementary data of your article and discrete diffusion model was selected. should i keep the substitution/clock/tree prior model default. ? for conventional beast analysis i used to select the substitution model as Best Model based on BIC. I am sorry for asking too much . Your help is really appreciated

sdellicour commented 12 months ago

When you specify such a fixed tree topology, you don't have to set those models. See for instance the XML file we prepared for the preliminary discrete phylogeographic analysis we conducted in that study: https://raw.githubusercontent.com/sdellicour/sars_cov_2_pipeline/master/TreeTime_100620.xml

Best,

Simon

Sikandar37 commented 12 months ago

Dear Simon, Thank you for your time and cooperation. I have solved the issue following your instructions and the XML file you provided was a great help for me. Now All the parameters of my analysis are well converged. Thank you once again