Table 1.
Current content in phylomeDB
| Phylome code | Seed species | Seed proteins | Species content | Total trees | Phylogenetic methods | Brief description |
|---|---|---|---|---|---|---|
| Hsapiens001 | Homo sapiens | 21 588 | 38 | 157 233 | NJ, Bayesian ML(JTT,WAG,B62, RtREV, MtREv) | 38 eukaryotic species from Ensembl, Integr8 and 3 other sources. |
| Ecoli001 | E. coli | 4604 | 421 | 9280 | NJ,ML(JTT,WAG) | 421 eukaryotic, archaeal and bacterial species from Integr8. |
| Scerevisiae001 | S. cerevisiae | 5811 | 421 | 5811 | NJ,ML(JTT) | The same species set as Ecoli001 |
| Total | 32 003 | 443 | 172 324 |
For each phylome included in the current release of PhylomeDB, the PhylomeDB internal code, the number of seed proteins, the number of species included, the total number of phylogenetic trees, the phylogenetic reconstruction methods and a brief description is provided. Phylogenetic methods are indicated as follows: Neighbor Joining (NJ), Bayesian analysis (Bayesian) and Maximum Likelihood (ML), which can be performed using JTT, WAG, Blosum62 (B62), RtREV and MtREV evolutionary models. Bayesian analysis was always performed using the evolutionary model that rendered the best likelihood in the ML analysis.