Phylogenetic reconstruction and functional characterization of the ancestral Nef protein of primate lentiviruses
Bibliographic record
Abstract
Supplementary data accompanying the manuscript "Phylogenetic reconstruction and functional characterization of the ancestral Nef protein of primate lentiviruses". group_m_ancestry_consensus_gaps_removed.afa - consensus amino acid sequences for ancestral reconstructions at the six internal nodes in FASTA format node35.fa.mafft - multiple sequence alignment of ancestral amino acid sequence reconstructions at the root of the primate lentivirus phylogeny (node 35) for 1,000 trees sampled from the posterior distribution node51.fa.mafft - multiple sequence alignment of ancestral amino acid sequence reconstructions for the common ancestor of HIV-1 and SIVsun (node 51) for 1,000 trees sampled from the posterior distribution node52.fa.mafft - multiple sequence alignment of ancestral amino acid sequence reconstructions for the common ancestor of HIV-1 and SIVcpz (node 52) for 1,000 trees sampled from the posterior distribution node55.fa.mafft - multiple sequence alignment of ancestral amino acid sequence reconstructions for the common ancestor of HIV-1 and SIVcpzptt (node 55) for 1,000 trees sampled from the posterior distribution node56.fa.mafft - multiple sequence alignment of ancestral amino acid sequence reconstructions for the common ancestor of HIV-1 groups M and N and SIVcpzptt (node 56) for 1,000 trees sampled from the posterior distribution node59.fa.mafft - multiple sequence alignment of ancestral amino acid sequence reconstructions for the common ancestor of HIV-1 group M (node 59) for 1,000 trees sampled from the posterior distribution
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.065 | 0.013 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".