Newick Trees for EMERGE methanogen genome tree, and methylotrophic gene trees ...
Newick trees provided for phylogenomic and phylogenetic analyses from Ellenbogen et al. (in prep). The methanogen genome tree (gtdbtk.ar53.decorated.tree) was built using a GTDB-Tk v12.1.1 r207 run with the de novo workflow. All other trees are RAxML gene trees built using ProtPipeliner (https://git...
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| Format: | Dataset |
| Language: | unknown |
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Zenodo
2023
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| Online Access: | https://dx.doi.org/10.5281/zenodo.7864933 https://zenodo.org/record/7864933 |
| Summary: | Newick trees provided for phylogenomic and phylogenetic analyses from Ellenbogen et al. (in prep). The methanogen genome tree (gtdbtk.ar53.decorated.tree) was built using a GTDB-Tk v12.1.1 r207 run with the de novo workflow. All other trees are RAxML gene trees built using ProtPipeliner (https://github.com/TheWrightonLab/Protpipeliner/blob/master/protpipeliner.py) to confirm the functional identity of identified methylotrophic genes from methanogens and bacteria. The names of the Newick trees correspond to relevant gene groupings as discussed in the associated manuscript. DRAM v1.3.2 raw annotations files for Stordalen methanogen MAGs also included. FUNDING: This research is a contribution of the EMERGE Biology Integration Institute, funded by the National Science Foundation, Biology Integration Institutes Program, Award # 2022070. We thank the Swedish Polar Research Secretariat and SITES for the support of the work done at the Abisko Scientific Research Station. SITES is supported by the Swedish Research ... |
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