Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation

- Introduced a comprehensive RNA velocity analysis pipeline using scVelo, including data loading, preprocessing, velocity estimation, and visualization.
- Added a script for running RNA velocity analysis with customizable parameters and output options.
- Created detailed documentation for IQ-TREE 2 phylogenetic inference, covering command syntax, model selection, bootstrapping methods, and output interpretation.
- Included references for velocity models and their mathematical framework, along with a comparison of different models.
- Enhanced the scVelo skill documentation with installation instructions, use cases, and best practices for RNA velocity analysis.

scientific-skills/interpro-database/references/domain_analysis.md

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+# InterPro Domain Analysis Reference
+
+## Entry Types
+
+| Type | Description | Example |
+|------|-------------|---------|
+| `family` | Group of related proteins sharing common evolutionary origin | IPR013872: p53 family |
+| `domain` | Distinct structural/functional unit that can exist independently | IPR011615: p53 tetramerisation domain |
+| `homologous_superfamily` | Proteins related by structure but not necessarily sequence | IPR009003: Peptidase, aspartic |
+| `repeat` | Short sequence unit that occurs in multiple copies | IPR000822: Ankyrin repeat |
+| `site` | Residues important for function | IPR018060: Metalloprotease active site |
+| `conserved_site` | Conserved sequence motif (functional) | IPR016152: PTB/PI domain binding site |
+| `active_site` | Catalytic residues | IPR000743: RING domain |
+| `binding_site` | Residues involved in binding | — |
+| `ptm` | Post-translational modification site | — |
+
+## Common Domain Accessions
+
+### Signaling Domains
+
+| Accession | Name | Function |
+|-----------|------|---------|
+| IPR000719 | Protein kinase domain | ATP-dependent phosphorylation |
+| IPR001245 | Serine-threonine/tyrosine-protein kinase | Kinase catalytic domain |
+| IPR000980 | SH2 domain | Phosphotyrosine binding |
+| IPR001452 | SH3 domain | Proline-rich sequence binding |
+| IPR011993 | PH domain | Phosphoinositide binding |
+| IPR000048 | IQ motif | Calmodulin binding |
+| IPR000008 | C2 domain | Ca2+/phospholipid binding |
+| IPR001849 | PH domain | Pleckstrin homology |
+
+### DNA Binding Domains
+
+| Accession | Name | Function |
+|-----------|------|---------|
+| IPR013087 | Zinc finger, C2H2 | DNA binding |
+| IPR017456 | CCCH zinc finger | RNA binding |
+| IPR011991 | Winged helix-turn-helix | Transcription factor DNA binding |
+| IPR011607 | MH1 domain | SMAD DNA binding |
+| IPR003313 | ARID domain | AT-rich DNA binding |
+| IPR014756 | E1-E2 ATPase, nucleotide-binding | — |
+
+### Structural Domains
+
+| Accession | Name | Function |
+|-----------|------|---------|
+| IPR001357 | BRCT domain | DNA repair protein interaction |
+| IPR000536 | Nuclear hormone receptor, ligand-binding | Hormone binding |
+| IPR001628 | Zinc finger, nuclear hormone receptor | DNA binding (NHR) |
+| IPR003961 | Fibronectin type III | Cell adhesion |
+| IPR000742 | EGF-like domain | Receptor-ligand interaction |
+
+## Domain Architecture Patterns
+
+Common multi-domain architectures and their biological meanings:
+
+### Receptor Tyrosine Kinases
+```
+[EGF domain]... - [TM] - [Kinase domain]
+e.g., EGFR: IPR000742 (EGF) + IPR000719 (kinase)
+```
+
+### Adapter Proteins
+```
+[SH3] - [SH2] - [SH3]
+e.g., Grb2, Crk — signaling adapters
+```
+
+### Nuclear Receptors
+```
+[DBD/C2H2 zinc finger] - [Ligand binding domain]
+e.g., ERα (ESR1)
+```
+
+### Kinases
+```
+[N-lobe] - [Activation loop] - [C-lobe]
+Standard protein kinase fold (IPR000719)
+```
+
+## GO Term Categories
+
+InterPro GO annotations use three ontologies:
+
+| Code | Ontology | Examples |
+|------|----------|---------|
+| P | Biological Process | GO:0006468 (protein phosphorylation) |
+| F | Molecular Function | GO:0004672 (protein kinase activity) |
+| C | Cellular Component | GO:0005886 (plasma membrane) |
+
+## InterProScan for Novel Sequences
+
+For protein sequences not in UniProt (novel/predicted sequences), run InterProScan:
+
+```bash
+# Command-line (install InterProScan locally)
+./interproscan.sh -i my_proteins.fasta -f tsv,json -dp
+
+# Options:
+# -i: input FASTA
+# -f: output formats (tsv, json, xml, gff3, html)
+# -dp: disable precalculation lookup (use for non-UniProt sequences)
+# --goterms: include GO term mappings
+# --pathways: include pathway mappings
+
+# Or use the web service:
+# https://www.ebi.ac.uk/interpro/search/sequence/
+```
+
+**Output fields (TSV):**
+1. Protein accession
+2. Sequence MD5
+3. Sequence length
+4. Analysis (e.g., Pfam, SMART)
+5. Signature accession (e.g., PF00397)
+6. Signature description
+7. Start
+8. Stop
+9. Score
+10. Status (T = true)
+11. Date
+12. InterPro accession (if integrated)
+13. InterPro description
+
+## Useful Entry ID Collections
+
+### Human Disease-Relevant Domains
+
+```python
+DISEASE_DOMAINS = {
+    # Cancer
+    "IPR011615": "p53 tetramerization",
+    "IPR012346": "p53/p63/p73, tetramerization domain",
+    "IPR000719": "Protein kinase domain",
+    "IPR004827": "Basic-leucine zipper (bZIP) TF",
+
+    # Neurodegenerative
+    "IPR003527": "MAP kinase, ERK1/2",
+    "IPR016024": "ARM-type fold",
+
+    # Metabolic
+    "IPR001764": "Glycoside hydrolase, family 13 (amylase)",
+    "IPR006047": "Glycoside hydrolase superfamily",
+}
+```
+
+### Commonly Referenced Pfam IDs
+
+| Pfam ID | Domain Name |
+|---------|-------------|
+| PF00069 | Pkinase (protein kinase) |
+| PF00076 | RRM_1 (RNA recognition motif) |
+| PF00096 | zf-C2H2 (zinc finger) |
+| PF00397 | WW domain |
+| PF00400 | WD40 repeat |
+| PF00415 | RasGEF domain |
+| PF00018 | SH3 domain |
+| PF00017 | SH2 domain |
+| PF02196 | zf-C3HC4 (RING finger) |