For example, for very diverse datasets of strains, the average branch support, even of the genome-based phylogeny, might be too low which is not unlikely for such datasets. In general, if certain parts in any given phylogeny are not well resolved (i.e. low branch support), these parts are not interpretable.
In case of the TYGS, an optional proteome-based GBDP analysis will become available on user request if the dataset is not too large (less than 30 strains) and the average branch support of the genome-based tree is smaller than 60%. If these conditions are met, you will find an order button on the respective TYGS result page below the phylogenies table. If the order button is not visible due to the above criteria, you can use the feedback form and ask for manually triggering the proteome-based reconstruction.
The method behind proteome-based GBDP analyses is similiar to the nucleotide-based GBDP analyses except for the use of the entire proteome in the former case. The method has been described here and here and, moreover, has been successfully applied in large-scale phylogenomic studies such as:
1. Lagkouvardos I, Pukall R, Abt B, Foesel BU, Meier-Kolthoff JP, Kumar N, et al. The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nat Microbiol. 2016;1: 16131. doi:10.1038/nmicrobiol.2016.131
2. Barka EA, Vatsa P, Sanchez L, Gaveau-vaillant N, Jacquard C, Meier-Kolthoff JP, et al. Taxonomy, physiology, and natural products of Actinobacteria. Microbiol Mol Biol Rev. 2016;80: iii. doi:10.1128/MMBR.00044-16
3. Nouioui I, Ghodhbane-Gtari F, Montero-Calasanz M del C, Göker M, Meier-Kolthoff JP, Schumann P, et al. Proposal of a type strain for Frankia alni ( Woronin 1866 ) Von Tubeuf 1895 , emended description of Frankia alni, and recognition of Frankia casuarinae sp. nov. and Frankia elaeagni sp. Int J Syst Evol Microbiol. 2016;published. doi:10.1099/ijsem.0.001496
4. Hahnke RL, Meier-Kolthoff JP, García-Lopez M, Mukherjee S, Huntemann M, Ivanova NN, et al. Genome-based taxonomic classification of Bacteroidetes. Front Microbiol. 2016;7: 2003. doi:10.3389/fmicb.2016.02003
5. Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I, Ulbrich M, et al. Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. ISME J. 2017;11: 1483–1499. doi:10.1038/ismej.2016.198
6. Montero-Calasanz M del C, Meier-Kolthoff JP, Zhang DF, Yaramis A, Rohde M, Woyke T, et al. Genome-scale data call for a taxonomic rearrangement ofGeodermatophilaceae. Front Microbiol. 2017;8: 1–15. doi:10.3389/fmicb.2017.02501
7. Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, et al. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nat Biotechnol. 2017;35: 676–683. doi:10.1038/nbt.3886
8. Carro L, Nouioui I, Sangal V, Meier-Kolthoff JP, Trujillo ME, Montero-Calasanz M del C, et al. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci Rep. 2018;8: 525. doi:10.1038/s41598-017-17392-0
9. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, et al. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol. 2018;9: 1–119. doi:10.3389/fmicb.2018.02007
10. García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, et al. Analysis of 1,000 type-strain genomes improves taxonomic classification of Bacteroidetes. Front Microbiol. 2019;10: 2083. doi:10.3389/fmicb.2019.02083
11. Hördt A, García-López M, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, et al. Analysis of 1,000+ type-strain genomes substantially improves taxonomic classification of Alphaproteobacteria. Front Microbiol. 2020;11: 468. doi:10.3389/fmicb.2020.00468
12. Dedysh SN, Henke P, Ivanova AA, Kulichevskaya IS, Philippov DA, Meier-Kolthoff JP, et al. 100-year-old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii. Environ Microbiol. 2020;22: 198–211. doi:10.1111/1462-2920.14838
13. Strepis N, Naranjo HD, Meier-Kolthoff J, Göker M, Shapiro N, Kyrpides N, et al. Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species. BMC Genomics. 2020;21: 1–13. doi:10.1186/s12864-019-6410-x
14. Schumann P, Kalensee F, Cao J, Criscuolo A, Clermont D, Köhler JM, et al. Reclassification of Haloactinobacterium glacieicola as Occultella glacieicola gen. nov., comb. nov., of Haloactinobacterium album as Ruania alba comb. nov, with an emended description of the genus Ruania, recognition that the genus names Haloactinobacteri. Int J Syst Evol Microbiol. 2021;71. doi:https://doi.org/10.1099/ijsem.0.004769
15. Heidler von Heilborn D, Reinmüller J, Hölzl G, Meier-Kolthoff JP, Woehle C, Marek M, et al. Sphingomonas aliaeris sp . nov ., a new species isolated from pork steak packed under modified atmosphere. Int J Syst Evol Microbiol. 2021;71: 004973. doi:10.1099/ijsem.0.004973