etetoolkit

Name: etetoolkit
Author: K-Dense-AI

31kstars3.1kforks

How to install etetoolkit?

k-dense-ai/scientific-agent-skills/etetoolkit

$npx -y skills add K-Dense-AI/scientific-agent-skills --skill etetoolkit

Installs into the current project.

Summary

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

Files · 1

View on GitHub

SKILL.md

1	# ETE Toolkit Skill
2
3	## Overview
4
5	ETE (Environment for Tree Exploration) is a toolkit for phylogenetic and hierarchical tree analysis. Manipulate trees, analyze evolutionary events, visualize results, and integrate with biological databases for phylogenomic research and clustering analysis.
6
7	## Core Capabilities
8
9	### 1. Tree Manipulation and Analysis
10
11	Load, manipulate, and analyze hierarchical tree structures with support for:
12
13	- Tree I/O: Read and write Newick, NHX, PhyloXML, and NeXML formats
14	- Tree traversal: Navigate trees using preorder, postorder, or levelorder strategies
15	- Topology modification: Prune, root, collapse nodes, resolve polytomies
16	- Distance calculations: Compute branch lengths and topological distances between nodes
17	- Tree comparison: Calculate Robinson-Foulds distances and identify topological differences
18
19	Common patterns:
20
21	```python
22	from ete3 import Tree
23
24	# Load tree from file
25	tree = Tree("tree.nw", format=1)
26
27	# Basic statistics
28	print(f"Leaves: {len(tree)}")
29	print(f"Total nodes: {len(list(tree.traverse()))}")
30
31	# Prune to taxa of interest
32	taxa_to_keep = ["species1", "species2", "species3"]
33	tree.prune(taxa_to_keep, preserve_branch_length=True)
34
35	# Midpoint root
36	midpoint = tree.get_midpoint_outgroup()
37	tree.set_outgroup(midpoint)
38
39	# Save modified tree
40	tree.write(outfile="rooted_tree.nw")
41	```
42
43	Use `scripts/tree_operations.py` for command-line tree manipulation:
44
45	```bash
46	# Display tree statistics
47	python scripts/tree_operations.py stats tree.nw
48
49	# Convert format
50	python scripts/tree_operations.py convert tree.nw output.nw --in-format 0 --out-format 1
51
52	# Reroot tree
53	python scripts/tree_operations.py reroot tree.nw rooted.nw --midpoint
54
55	# Prune to specific taxa
56	python scripts/tree_operations.py prune tree.nw pruned.nw --keep-taxa "sp1,sp2,sp3"
57
58	# Show ASCII visualization
59	python scripts/tree_operations.py ascii tree.nw
60	```
61
62	### 2. Phylogenetic Analysis
63
64	Analyze gene trees with evolutionary event detection:
65
66	- Sequence alignment integration: Link trees to multiple sequence alignments (FASTA, Phylip)
67	- Species naming: Automatic or custom species extraction from gene names
68	- Evolutionary events: Detect duplication and speciation events using Species Overlap or tree reconciliation
69	- Orthology detection: Identify orthologs and paralogs based on evolutionary events
70	- Gene family analysis: Split trees by duplications, collapse lineage-specific expansions
71
72	Workflow for gene tree analysis:
73
74	```python
75	from ete3 import PhyloTree
76
77	# Load gene tree with alignment
78	tree = PhyloTree("gene_tree.nw", alignment="alignment.fasta")
79
80	# Set species naming function
81	def get_species(gene_name):
82	return gene_name.split("_")[0]
83
84	tree.set_species_naming_function(get_species)
85
86	# Detect evolutionary events
87	events = tree.get_descendant_evol_events()
88
89	# Analyze events
90	for node in tree.traverse():
91	if hasattr(node, "evoltype"):
92	if node.evoltype == "D":
93	print(f"Duplication at {node.name}")
94	elif node.evoltype == "S":
95	print(f"Speciation at {node.name}")
96
97	# Extract ortholog groups
98	ortho_groups = tree.get_speciation_trees()
99	for i, ortho_tree in enumerate(ortho_groups):
100	ortho_tree.write(outfile=f"ortholog_group_{i}.nw")
101	```
102
103	Finding orthologs and paralogs:
104
105	```python
106	# Find orthologs to query gene
107	query = tree & "species1_gene1"
108
109	orthologs = []
110	paralogs = []
111
112	for event in events:
113	if query in event.in_seqs:
114	if event.etype == "S":
115	orthologs.extend([s for s in event.out_seqs if s != query])
116	elif event.etype == "D":
117	paralogs.extend([s for s in event.out_seqs if s != query])
118	```
119
120	### 3. NCBI Taxonomy Integration
121
122	Integrate taxonomic information from NCBI Taxonomy database:
123
124	- Database access: Automatic download and local caching of NCBI taxonomy (~300MB)
125	- Taxid/name translation: Convert between taxonomic IDs and scientific names
126	- Lineage retrieval: Get complete evolutionary lineages
127	- Taxonomy trees: Build species trees connecting specified taxa
128	- Tree annotation: Automatically annotate trees with taxonomic information
129
130	Building taxonomy-based trees:
131
132	```python
133	from ete3 import NCBITaxa
134
135	ncbi = NCBITaxa()
136
137	# Build tree from species names
138	species = ["Homo sapiens", "Pan troglodytes", "Mus musculus"]
139	name2taxid = ncbi.get_name_translator(species)
140	taxids = [name2taxid[sp][0] for sp in species]
141
142	# Get minimal tree connecting taxa
143	tree = ncbi.get_topology(taxids)
144
145	# Annotate nodes with taxonomy info
146	for node in tree.traverse():
147	if hasattr(node, "sci_name"):
148	print(f"{node.sci_name} - Rank: {node.rank} - TaxID: {node.taxid}")
149	```
150
151	Annotating existing trees:
152
153	```python
154	#

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etetoolkit

31kstars3.1kforks

View on GitHub

How to install etetoolkit?

k-dense-ai/scientific-agent-skills/etetoolkit

$npx -y skills add K-Dense-AI/scientific-agent-skills --skill etetoolkit

Installs into the current project.

Summary

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

Files · 1

View on GitHub

SKILL.md

1	# ETE Toolkit Skill
2
3	## Overview
4
5	ETE (Environment for Tree Exploration) is a toolkit for phylogenetic and hierarchical tree analysis. Manipulate trees, analyze evolutionary events, visualize results, and integrate with biological databases for phylogenomic research and clustering analysis.
6
7	## Core Capabilities
8
9	### 1. Tree Manipulation and Analysis
10
11	Load, manipulate, and analyze hierarchical tree structures with support for:
12
13	- Tree I/O: Read and write Newick, NHX, PhyloXML, and NeXML formats
14	- Tree traversal: Navigate trees using preorder, postorder, or levelorder strategies
15	- Topology modification: Prune, root, collapse nodes, resolve polytomies
16	- Distance calculations: Compute branch lengths and topological distances between nodes
17	- Tree comparison: Calculate Robinson-Foulds distances and identify topological differences
18
19	Common patterns:
20
21	```python
22	from ete3 import Tree
23
24	# Load tree from file
25	tree = Tree("tree.nw", format=1)
26
27	# Basic statistics
28	print(f"Leaves: {len(tree)}")
29	print(f"Total nodes: {len(list(tree.traverse()))}")
30
31	# Prune to taxa of interest
32	taxa_to_keep = ["species1", "species2", "species3"]
33	tree.prune(taxa_to_keep, preserve_branch_length=True)
34
35	# Midpoint root
36	midpoint = tree.get_midpoint_outgroup()
37	tree.set_outgroup(midpoint)
38
39	# Save modified tree
40	tree.write(outfile="rooted_tree.nw")
41	```
42
43	Use `scripts/tree_operations.py` for command-line tree manipulation:
44
45	```bash
46	# Display tree statistics
47	python scripts/tree_operations.py stats tree.nw
48
49	# Convert format
50	python scripts/tree_operations.py convert tree.nw output.nw --in-format 0 --out-format 1
51
52	# Reroot tree
53	python scripts/tree_operations.py reroot tree.nw rooted.nw --midpoint
54
55	# Prune to specific taxa
56	python scripts/tree_operations.py prune tree.nw pruned.nw --keep-taxa "sp1,sp2,sp3"
57
58	# Show ASCII visualization
59	python scripts/tree_operations.py ascii tree.nw
60	```
61
62	### 2. Phylogenetic Analysis
63
64	Analyze gene trees with evolutionary event detection:
65
66	- Sequence alignment integration: Link trees to multiple sequence alignments (FASTA, Phylip)
67	- Species naming: Automatic or custom species extraction from gene names
68	- Evolutionary events: Detect duplication and speciation events using Species Overlap or tree reconciliation
69	- Orthology detection: Identify orthologs and paralogs based on evolutionary events
70	- Gene family analysis: Split trees by duplications, collapse lineage-specific expansions
71
72	Workflow for gene tree analysis:
73
74	```python
75	from ete3 import PhyloTree
76
77	# Load gene tree with alignment
78	tree = PhyloTree("gene_tree.nw", alignment="alignment.fasta")
79
80	# Set species naming function
81	def get_species(gene_name):
82	return gene_name.split("_")[0]
83
84	tree.set_species_naming_function(get_species)
85
86	# Detect evolutionary events
87	events = tree.get_descendant_evol_events()
88
89	# Analyze events
90	for node in tree.traverse():
91	if hasattr(node, "evoltype"):
92	if node.evoltype == "D":
93	print(f"Duplication at {node.name}")
94	elif node.evoltype == "S":
95	print(f"Speciation at {node.name}")
96
97	# Extract ortholog groups
98	ortho_groups = tree.get_speciation_trees()
99	for i, ortho_tree in enumerate(ortho_groups):
100	ortho_tree.write(outfile=f"ortholog_group_{i}.nw")
101	```
102
103	Finding orthologs and paralogs:
104
105	```python
106	# Find orthologs to query gene
107	query = tree & "species1_gene1"
108
109	orthologs = []
110	paralogs = []
111
112	for event in events:
113	if query in event.in_seqs:
114	if event.etype == "S":
115	orthologs.extend([s for s in event.out_seqs if s != query])
116	elif event.etype == "D":
117	paralogs.extend([s for s in event.out_seqs if s != query])
118	```
119
120	### 3. NCBI Taxonomy Integration
121
122	Integrate taxonomic information from NCBI Taxonomy database:
123
124	- Database access: Automatic download and local caching of NCBI taxonomy (~300MB)
125	- Taxid/name translation: Convert between taxonomic IDs and scientific names
126	- Lineage retrieval: Get complete evolutionary lineages
127	- Taxonomy trees: Build species trees connecting specified taxa
128	- Tree annotation: Automatically annotate trees with taxonomic information
129
130	Building taxonomy-based trees:
131
132	```python
133	from ete3 import NCBITaxa
134
135	ncbi = NCBITaxa()
136
137	# Build tree from species names
138	species = ["Homo sapiens", "Pan troglodytes", "Mus musculus"]
139	name2taxid = ncbi.get_name_translator(species)
140	taxids = [name2taxid[sp][0] for sp in species]
141
142	# Get minimal tree connecting taxa
143	tree = ncbi.get_topology(taxids)
144
145	# Annotate nodes with taxonomy info
146	for node in tree.traverse():
147	if hasattr(node, "sci_name"):
148	print(f"{node.sci_name} - Rank: {node.rank} - TaxID: {node.taxid}")
149	```
150
151	Annotating existing trees:
152
153	```python
154	#

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