advanced-phylogeny

Name: advanced-phylogeny
Author: KevinSpringer1

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How to install advanced-phylogeny?

kevinspringer1/conserved-primer-design/advanced-phylogeny

$npx -y skills add KevinSpringer1/conserved-primer-design --skill advanced-phylogeny

Installs into the current project.

Summary

Use when an agent needs a stricter or publication-grade phylogeny workflow for PhyloGuide, including tree/MSA validation, FastTree/IQ-TREE planning, and external-tree checks.

Files · 1

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SKILL.md

1	# Advanced Phylogeny
2
3	Use this when `prepare-phylo`'s deterministic p-distance neighbor-joining tree is insufficient for the species, dataset, or reporting standard.
4
5	## Tool Plan
6
7	```bash
8	python agentskill/scripts/advanced_phylogeny.py tool-plan \
9	--output phylo_tool_plan.json
10	```
11
12	## Validate External Tree
13
14	Always validate the final Newick against the exact aligned FASTA IDs before `phylo_guide` submission:
15
16	```bash
17	python agentskill/scripts/advanced_phylogeny.py validate-tree \
18	--msa aligned.normalized.fasta \
19	--tree tree.newick \
20	--output tree_validation.json
21	```
22
23	## Optional External Trees
24
25	Run only when tools are installed:
26
27	```bash
28	python agentskill/scripts/advanced_phylogeny.py run-fasttree \
29	--msa aligned.normalized.fasta \
30	--output-tree fasttree.newick \
31	--report fasttree_report.json
32
33	python agentskill/scripts/advanced_phylogeny.py run-iqtree \
34	--msa aligned.normalized.fasta \
35	--prefix iqtree_run \
36	--bootstrap 1000 \
37	--report iqtree_report.json
38	```
39
40	Use literature/curated taxonomy to define groups; a tree alone does not justify genotype labels.

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advanced-phylogeny

30stars0forks

View on GitHub

How to install advanced-phylogeny?

kevinspringer1/conserved-primer-design/advanced-phylogeny

$npx -y skills add KevinSpringer1/conserved-primer-design --skill advanced-phylogeny

Installs into the current project.

Summary

Use when an agent needs a stricter or publication-grade phylogeny workflow for PhyloGuide, including tree/MSA validation, FastTree/IQ-TREE planning, and external-tree checks.

Files · 1

View on GitHub

SKILL.md

1	# Advanced Phylogeny
2
3	Use this when `prepare-phylo`'s deterministic p-distance neighbor-joining tree is insufficient for the species, dataset, or reporting standard.
4
5	## Tool Plan
6
7	```bash
8	python agentskill/scripts/advanced_phylogeny.py tool-plan \
9	--output phylo_tool_plan.json
10	```
11
12	## Validate External Tree
13
14	Always validate the final Newick against the exact aligned FASTA IDs before `phylo_guide` submission:
15
16	```bash
17	python agentskill/scripts/advanced_phylogeny.py validate-tree \
18	--msa aligned.normalized.fasta \
19	--tree tree.newick \
20	--output tree_validation.json
21	```
22
23	## Optional External Trees
24
25	Run only when tools are installed:
26
27	```bash
28	python agentskill/scripts/advanced_phylogeny.py run-fasttree \
29	--msa aligned.normalized.fasta \
30	--output-tree fasttree.newick \
31	--report fasttree_report.json
32
33	python agentskill/scripts/advanced_phylogeny.py run-iqtree \
34	--msa aligned.normalized.fasta \
35	--prefix iqtree_run \
36	--bootstrap 1000 \
37	--report iqtree_report.json
38	```
39
40	Use literature/curated taxonomy to define groups; a tree alone does not justify genotype labels.

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6 picks

Type