René's URL Explorer Experiment

Title: GitHub - DessimozLab/read2tree: a tool for inferring species tree from sequencing reads

Open Graph Title: GitHub - DessimozLab/read2tree: a tool for inferring species tree from sequencing reads

X Title: GitHub - DessimozLab/read2tree: a tool for inferring species tree from sequencing reads

Description: a tool for inferring species tree from sequencing reads - DessimozLab/read2tree

Open Graph Description: a tool for inferring species tree from sequencing reads - DessimozLab/read2tree

X Description: a tool for inferring species tree from sequencing reads - DessimozLab/read2tree

Opengraph URL: https://github.com/DessimozLab/read2tree

X: @github

direct link

Domain: patch-diff.githubusercontent.com

route-pattern	/:user_id/:repository
route-controller	files
route-action	disambiguate
fetch-nonce	v2:b4e8eb9c-9954-ba4c-f9bb-29228ecf083b
current-catalog-service-hash	f3abb0cc802f3d7b95fc8762b94bdcb13bf39634c40c357301c4aa1d67a256fb
request-id	D712:34E4BD:2ADF12C:3BABC36:6977AF87
html-safe-nonce	ec0693167ced07618974da515fdeb3d7ecf516d1793b15af63ce7dca6c5e2195
visitor-payload	eyJyZWZlcnJlciI6IiIsInJlcXVlc3RfaWQiOiJENzEyOjM0RTRCRDoyQURGMTJDOjNCQUJDMzY6Njk3N0FGODciLCJ2aXNpdG9yX2lkIjoiNzc5NjI3MTA4MzI0NDk5MDM0MyIsInJlZ2lvbl9lZGdlIjoiaWFkIiwicmVnaW9uX3JlbmRlciI6ImlhZCJ9
visitor-hmac	643244a2d48a339f53883e498d8843395ec27cff08cc16855d444b4d165dfd03
hovercard-subject-tag	repository:481189531
github-keyboard-shortcuts	repository,copilot
google-site-verification	Apib7-x98H0j5cPqHWwSMm6dNU4GmODRoqxLiDzdx9I
octolytics-url	https://collector.github.com/github/collect
analytics-location	//
fb:app_id	1401488693436528
apple-itunes-app	app-id=1477376905, app-argument=https://github.com/DessimozLab/read2tree
twitter:image	https://opengraph.githubassets.com/8c618c7a9a3f0827feda1d981445cecc08b44b30b81b5b976869062615024bc4/DessimozLab/read2tree
twitter:card	summary_large_image
og:image	https://opengraph.githubassets.com/8c618c7a9a3f0827feda1d981445cecc08b44b30b81b5b976869062615024bc4/DessimozLab/read2tree
og:image:alt	a tool for inferring species tree from sequencing reads - DessimozLab/read2tree
og:image:width	1200
og:image:height	600
og:site_name	GitHub
og:type	object
hostname	github.com
expected-hostname	github.com
None	cd86879038a75d35d75e56f263b8ad57328b023c6a7de3aa5f9ca0dfd46935bb
turbo-cache-control	no-preview
go-import	github.com/DessimozLab/read2tree git https://github.com/DessimozLab/read2tree.git
octolytics-dimension-user_id	16049503
octolytics-dimension-user_login	DessimozLab
octolytics-dimension-repository_id	481189531
octolytics-dimension-repository_nwo	DessimozLab/read2tree
octolytics-dimension-repository_public	true
octolytics-dimension-repository_is_fork	false
octolytics-dimension-repository_network_root_id	481189531
octolytics-dimension-repository_network_root_nwo	DessimozLab/read2tree
turbo-body-classes	logged-out env-production page-responsive
disable-turbo	false
browser-stats-url	https://api.github.com/_private/browser/stats
browser-errors-url	https://api.github.com/_private/browser/errors
release	8458c691435c924883b72423ecd12134159e1b18
ui-target	full
theme-color	#1e2327
color-scheme	light dark

Links:

Skip to content	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#start-of-content
	https://patch-diff.githubusercontent.com/
Sign in	https://patch-diff.githubusercontent.com/login?return_to=https%3A%2F%2Fgithub.com%2FDessimozLab%2Fread2tree
GitHub CopilotWrite better code with AI	https://github.com/features/copilot
GitHub SparkBuild and deploy intelligent apps	https://github.com/features/spark
GitHub ModelsManage and compare prompts	https://github.com/features/models
MCP RegistryNewIntegrate external tools	https://github.com/mcp
ActionsAutomate any workflow	https://github.com/features/actions
CodespacesInstant dev environments	https://github.com/features/codespaces
IssuesPlan and track work	https://github.com/features/issues
Code ReviewManage code changes	https://github.com/features/code-review
GitHub Advanced SecurityFind and fix vulnerabilities	https://github.com/security/advanced-security
Code securitySecure your code as you build	https://github.com/security/advanced-security/code-security
Secret protectionStop leaks before they start	https://github.com/security/advanced-security/secret-protection
Why GitHub	https://github.com/why-github
Documentation	https://docs.github.com
Blog	https://github.blog
Changelog	https://github.blog/changelog
Marketplace	https://github.com/marketplace
View all features	https://github.com/features
Enterprises	https://github.com/enterprise
Small and medium teams	https://github.com/team
Startups	https://github.com/enterprise/startups
Nonprofits	https://github.com/solutions/industry/nonprofits
App Modernization	https://github.com/solutions/use-case/app-modernization
DevSecOps	https://github.com/solutions/use-case/devsecops
DevOps	https://github.com/solutions/use-case/devops
CI/CD	https://github.com/solutions/use-case/ci-cd
View all use cases	https://github.com/solutions/use-case
Healthcare	https://github.com/solutions/industry/healthcare
Financial services	https://github.com/solutions/industry/financial-services
Manufacturing	https://github.com/solutions/industry/manufacturing
Government	https://github.com/solutions/industry/government
View all industries	https://github.com/solutions/industry
View all solutions	https://github.com/solutions
AI	https://github.com/resources/articles?topic=ai
Software Development	https://github.com/resources/articles?topic=software-development
DevOps	https://github.com/resources/articles?topic=devops
Security	https://github.com/resources/articles?topic=security
View all topics	https://github.com/resources/articles
Customer stories	https://github.com/customer-stories
Events & webinars	https://github.com/resources/events
Ebooks & reports	https://github.com/resources/whitepapers
Business insights	https://github.com/solutions/executive-insights
GitHub Skills	https://skills.github.com
Documentation	https://docs.github.com
Customer support	https://support.github.com
Community forum	https://github.com/orgs/community/discussions
Trust center	https://github.com/trust-center
Partners	https://github.com/partners
GitHub SponsorsFund open source developers	https://github.com/sponsors
Security Lab	https://securitylab.github.com
Maintainer Community	https://maintainers.github.com
Accelerator	https://github.com/accelerator
Archive Program	https://archiveprogram.github.com
Topics	https://github.com/topics
Trending	https://github.com/trending
Collections	https://github.com/collections
Enterprise platformAI-powered developer platform	https://github.com/enterprise
GitHub Advanced SecurityEnterprise-grade security features	https://github.com/security/advanced-security
Copilot for BusinessEnterprise-grade AI features	https://github.com/features/copilot/copilot-business
Premium SupportEnterprise-grade 24/7 support	https://github.com/premium-support
Pricing	https://github.com/pricing
Search syntax tips	https://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax
documentation	https://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax
Sign in	https://patch-diff.githubusercontent.com/login?return_to=https%3A%2F%2Fgithub.com%2FDessimozLab%2Fread2tree
Sign up	https://patch-diff.githubusercontent.com/signup?ref_cta=Sign+up&ref_loc=header+logged+out&ref_page=%2F%3Cuser-name%3E%2F%3Crepo-name%3E&source=header-repo&source_repo=DessimozLab%2Fread2tree
Reload	https://patch-diff.githubusercontent.com/DessimozLab/read2tree
Reload	https://patch-diff.githubusercontent.com/DessimozLab/read2tree
Reload	https://patch-diff.githubusercontent.com/DessimozLab/read2tree
DessimozLab	https://patch-diff.githubusercontent.com/DessimozLab
read2tree	https://patch-diff.githubusercontent.com/DessimozLab/read2tree
Notifications	https://patch-diff.githubusercontent.com/login?return_to=%2FDessimozLab%2Fread2tree
Fork 19	https://patch-diff.githubusercontent.com/login?return_to=%2FDessimozLab%2Fread2tree
Star 156	https://patch-diff.githubusercontent.com/login?return_to=%2FDessimozLab%2Fread2tree
MIT license	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/blob/main/LICENSE
156 stars	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/stargazers
19 forks	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/forks
Branches	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/branches
Tags	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/tags
Activity	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/activity
Star	https://patch-diff.githubusercontent.com/login?return_to=%2FDessimozLab%2Fread2tree
Notifications	https://patch-diff.githubusercontent.com/login?return_to=%2FDessimozLab%2Fread2tree
Code	https://patch-diff.githubusercontent.com/DessimozLab/read2tree
Issues 22	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/issues
Pull requests 0	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/pulls
Actions	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/actions
Projects 0	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/projects
Wiki	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/wiki
Security 0	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/security
Insights	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/pulse
Code	https://patch-diff.githubusercontent.com/DessimozLab/read2tree
Issues	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/issues
Pull requests	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/pulls
Actions	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/actions
Projects	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/projects
Wiki	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/wiki
Security	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/security
Insights	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/pulse
Branches	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/branches
Tags	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/tags
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/branches
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/tags
588 Commits	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/commits/main/
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/commits/main/
.github/workflows	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/tree/main/.github/workflows
.github/workflows	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/tree/main/.github/workflows
archive	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/tree/main/archive
archive	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/tree/main/archive
bin	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/tree/main/bin
bin	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/tree/main/bin
read2tree	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/tree/main/read2tree
read2tree	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/tree/main/read2tree
src	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/tree/main/src
src	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/tree/main/src
tests	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/tree/main/tests
tests	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/tree/main/tests
.gitignore	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/blob/main/.gitignore
.gitignore	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/blob/main/.gitignore
Dockerfile	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/blob/main/Dockerfile
Dockerfile	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/blob/main/Dockerfile
LICENSE	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/blob/main/LICENSE
LICENSE	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/blob/main/LICENSE
README.md	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/blob/main/README.md
README.md	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/blob/main/README.md
environment.yml	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/blob/main/environment.yml
environment.yml	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/blob/main/environment.yml
setup.py	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/blob/main/setup.py
setup.py	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/blob/main/setup.py
README	https://patch-diff.githubusercontent.com/DessimozLab/read2tree
MIT license	https://patch-diff.githubusercontent.com/DessimozLab/read2tree
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#read2tree
	https://www.python.org/downloads/release/python-310/
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#new-release
minimap2	https://github.com/lh3/minimap2
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#read2tree-talk
in silico talks	https://www.sib.swiss/in-silico-talks/read2tree-inferring-phylogenetic-trees-from-raw-sequencing-data
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#read2tree-publication
Nature Biotechnology	https://doi.org/10.1038/s41587-023-01753-4
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#installation
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#1-installation-from-source
conda	https://docs.conda.io/en/latest/miniconda.html
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#prerequisites
numpy	https://github.com/numpy/numpy
scipy	https://github.com/scipy/scipy
cython	https://github.com/cython/cython
lxml	https://github.com/lxml/lxml
tqdm	https://tqdm.github.io/docs/tqdm
pysam	https://github.com/pysam-developers/pysam
pyparsing	https://svn.code.sf.net/p/pyparsing/code/
requests	http://python-requests.org
filelock	https://github.com/benediktschmitt/py-filelock
natsort	https://github.com/SethMMorton/natsort
pyyaml	http://pyyaml.org/wiki/PyYAML
biopython	https://github.com/biopython/biopython
ete3	http://etetoolkit.org
dendropy	http://packages.python.org/DendroPy/
mafft	http://mafft.cbrc.jp/alignment/software/
iqtree	http://www.iqtree.org/
minimap2	https://github.com/lh3/minimap2
samtools	http://www.htslib.org/download/
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#run
page	https://github.com/DessimozLab/read2tree/wiki/obtaining-marker-genes
OMA browser	https://omabrowser.org/oma/export_markers
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#output
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#single-species-mode
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#multiple-species-mode
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#step1
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#step2
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#step3
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#bootstraping
trimal	http://trimal.cgenomics.org/use_of_the_command_line_trimal_v1.2
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#dna-mode-tree-inference
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#test-example
SRR5171076	https://www.ncbi.nlm.nih.gov/sra/?term=SRR5171076
sra-tools	https://anaconda.org/bioconda/sra-tools
OMA browser	https://omabrowser.org/oma/export_markers
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#run-test-example-using-docker
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#output-files
page	https://github.com/DessimozLab/read2tree/wiki/output-files
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#details-of-arguments
page	https://github.com/DessimozLab/read2tree/wiki/Details-of-arguments
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#possible-issues
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#change-log
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#authors
David Dylus	https://github.com/dvdylus
Adrian Altenhoff	http://people.inf.ethz.ch/adriaal
Sina Majidian	https://sinamajidian.github.io/
	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#license
Readme	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#readme-ov-file
MIT license	https://patch-diff.githubusercontent.com/DessimozLab/read2tree#MIT-1-ov-file
Please reload this page	https://patch-diff.githubusercontent.com/DessimozLab/read2tree
Activity	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/activity
Custom properties	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/custom-properties
156 stars	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/stargazers
8 watching	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/watchers
19 forks	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/forks
Report repository	https://patch-diff.githubusercontent.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2FDessimozLab%2Fread2tree&report=DessimozLab+%28user%29
Releases 5	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/releases
v2.0.1 Latest Sep 23, 2025	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/releases/tag/v2.0.1
+ 4 releases	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/releases
Packages 0	https://patch-diff.githubusercontent.com/orgs/DessimozLab/packages?repo_name=read2tree
Please reload this page	https://patch-diff.githubusercontent.com/DessimozLab/read2tree
Contributors 5	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/graphs/contributors
Please reload this page	https://patch-diff.githubusercontent.com/DessimozLab/read2tree
Python 99.1%	https://patch-diff.githubusercontent.com/DessimozLab/read2tree/search?l=python
	https://github.com
Terms	https://docs.github.com/site-policy/github-terms/github-terms-of-service
Privacy	https://docs.github.com/site-policy/privacy-policies/github-privacy-statement
Security	https://github.com/security
Status	https://www.githubstatus.com/
Community	https://github.community/
Docs	https://docs.github.com/
Contact	https://support.github.com?tags=dotcom-footer

Viewport: width=device-width

URLs of crawlers that visited me.