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GitHub - DessimozLab/read2tree: a tool for inferring species tree from sequencing reads
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js-header-menu-item"> <button type="button" class="HeaderMenu-link border-0 width-full width-lg-auto px-0 px-lg-2 py-lg-2 no-wrap d-flex flex-items-center flex-justify-between js-details-target" aria-expanded="false"> Product <svg opacity="0.5" aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-chevron-down HeaderMenu-icon ml-1"> <path d="M12.78 5.22a.749.749 0 0 1 0 1.06l-4.25 4.25a.749.749 0 0 1-1.06 0L3.22 6.28a.749.749 0 1 1 1.06-1.06L8 8.939l3.72-3.719a.749.749 0 0 1 1.06 0Z"></path> </svg> </button> <div class="HeaderMenu-dropdown dropdown-menu rounded m-0 p-0 pt-2 pt-lg-4 position-relative position-lg-absolute left-0 left-lg-n3 pb-2 pb-lg-4 d-lg-flex flex-wrap dropdown-menu-wide"> <div class="HeaderMenu-column px-lg-4 border-lg-right mb-4 mb-lg-0 pr-lg-7"> <div class="border-bottom pb-3 pb-lg-0 border-lg-bottom-0"> <ul class="list-style-none f5" > <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" data-analytics-event="{"location":"navbar","action":"github_copilot","context":"product","tag":"link","label":"github_copilot_link_product_navbar"}" href="https://github.com/features/copilot"> <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-copilot color-fg-subtle mr-3"> <path d="M23.922 16.992c-.861 1.495-5.859 5.023-11.922 5.023-6.063 0-11.061-3.528-11.922-5.023A.641.641 0 0 1 0 16.736v-2.869a.841.841 0 0 1 .053-.22c.372-.935 1.347-2.292 2.605-2.656.167-.429.414-1.055.644-1.517a10.195 10.195 0 0 1-.052-1.086c0-1.331.282-2.499 1.132-3.368.397-.406.89-.717 1.474-.952 1.399-1.136 3.392-2.093 6.122-2.093 2.731 0 4.767.957 6.166 2.093.584.235 1.077.546 1.474.952.85.869 1.132 2.037 1.132 3.368 0 .368-.014.733-.052 1.086.23.462.477 1.088.644 1.517 1.258.364 2.233 1.721 2.605 2.656a.832.832 0 0 1 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0v-2a1 1 0 0 1 1-1Zm-5 0a1 1 0 0 1 1 1v2a1 1 0 0 1-2 0v-2a1 1 0 0 1 1-1Z"></path> </svg> <div> <div class="color-fg-default h4">GitHub Copilot</div> Write better code with AI </div> </a></li> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" data-analytics-event="{"location":"navbar","action":"security","context":"product","tag":"link","label":"security_link_product_navbar"}" href="https://github.com/features/security"> <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-shield-check color-fg-subtle mr-3"> <path d="M16.53 9.78a.75.75 0 0 0-1.06-1.06L11 13.19l-1.97-1.97a.75.75 0 0 0-1.06 1.06l2.5 2.5a.75.75 0 0 0 1.06 0l5-5Z"></path><path d="m12.54.637 8.25 2.675A1.75 1.75 0 0 1 22 4.976V10c0 6.19-3.771 10.704-9.401 12.83a1.704 1.704 0 0 1-1.198 0C5.77 20.705 2 16.19 2 10V4.976c0-.758.489-1.43 1.21-1.664L11.46.637a1.748 1.748 0 0 1 1.08 0Zm-.617 1.426-8.25 2.676a.249.249 0 0 0-.173.237V10c0 5.46 3.28 9.483 8.43 11.426a.199.199 0 0 0 .14 0C17.22 19.483 20.5 15.461 20.5 10V4.976a.25.25 0 0 0-.173-.237l-8.25-2.676a.253.253 0 0 0-.154 0Z"></path> </svg> <div> <div class="color-fg-default h4">Security</div> Find and fix vulnerabilities </div> </a></li> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" data-analytics-event="{"location":"navbar","action":"actions","context":"product","tag":"link","label":"actions_link_product_navbar"}" href="https://github.com/features/actions"> <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-workflow color-fg-subtle mr-3"> <path d="M1 3a2 2 0 0 1 2-2h6.5a2 2 0 0 1 2 2v6.5a2 2 0 0 1-2 2H7v4.063C7 16.355 7.644 17 8.438 17H12.5v-2.5a2 2 0 0 1 2-2H21a2 2 0 0 1 2 2V21a2 2 0 0 1-2 2h-6.5a2 2 0 0 1-2-2v-2.5H8.437A2.939 2.939 0 0 1 5.5 15.562V11.5H3a2 2 0 0 1-2-2Zm2-.5a.5.5 0 0 0-.5.5v6.5a.5.5 0 0 0 .5.5h6.5a.5.5 0 0 0 .5-.5V3a.5.5 0 0 0-.5-.5ZM14.5 14a.5.5 0 0 0-.5.5V21a.5.5 0 0 0 .5.5H21a.5.5 0 0 0 .5-.5v-6.5a.5.5 0 0 0-.5-.5Z"></path> </svg> <div> <div class="color-fg-default h4">Actions</div> Automate any workflow </div> </a></li> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" data-analytics-event="{"location":"navbar","action":"codespaces","context":"product","tag":"link","label":"codespaces_link_product_navbar"}" href="https://github.com/features/codespaces"> <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon octicon-codespaces color-fg-subtle mr-3"> <path d="M3.5 3.75C3.5 2.784 4.284 2 5.25 2h13.5c.966 0 1.75.784 1.75 1.75v7.5A1.75 1.75 0 0 1 18.75 13H5.25a1.75 1.75 0 0 1-1.75-1.75Zm-2 12c0-.966.784-1.75 1.75-1.75h17.5c.966 0 1.75.784 1.75 1.75v4a1.75 1.75 0 0 1-1.75 1.75H3.25a1.75 1.75 0 0 1-1.75-1.75ZM5.25 3.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h13.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Zm-2 12a.25.25 0 0 0-.25.25v4c0 .138.112.25.25.25h17.5a.25.25 0 0 0 .25-.25v-4a.25.25 0 0 0-.25-.25Z"></path><path d="M10 17.75a.75.75 0 0 1 .75-.75h6.5a.75.75 0 0 1 0 1.5h-6.5a.75.75 0 0 1-.75-.75Zm-4 0a.75.75 0 0 1 .75-.75h.5a.75.75 0 0 1 0 1.5h-.5a.75.75 0 0 1-.75-.75Z"></path> </svg> <div> <div class="color-fg-default h4">Codespaces</div> Instant dev environments </div> </a></li> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" data-analytics-event="{"location":"navbar","action":"issues","context":"product","tag":"link","label":"issues_link_product_navbar"}" href="https://github.com/features/issues"> <svg aria-hidden="true" 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6.74a.75.75 0 0 1-.04 1.06l-2.908 2.7 2.908 2.7a.75.75 0 1 1-1.02 1.1l-3.5-3.25a.75.75 0 0 1 0-1.1l3.5-3.25a.75.75 0 0 1 1.06.04Zm3.44 1.06a.75.75 0 1 1 1.02-1.1l3.5 3.25a.75.75 0 0 1 0 1.1l-3.5 3.25a.75.75 0 1 1-1.02-1.1l2.908-2.7-2.908-2.7Z"></path><path d="M1.5 4.25c0-.966.784-1.75 1.75-1.75h17.5c.966 0 1.75.784 1.75 1.75v12.5a1.75 1.75 0 0 1-1.75 1.75h-9.69l-3.573 3.573A1.458 1.458 0 0 1 5 21.043V18.5H3.25a1.75 1.75 0 0 1-1.75-1.75ZM3.25 4a.25.25 0 0 0-.25.25v12.5c0 .138.112.25.25.25h2.5a.75.75 0 0 1 .75.75v3.19l3.72-3.72a.749.749 0 0 1 .53-.22h10a.25.25 0 0 0 .25-.25V4.25a.25.25 0 0 0-.25-.25Z"></path> </svg> <div> <div class="color-fg-default h4">Code Review</div> Manage code changes </div> </a></li> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" 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2h16.5c.966 0 1.75.784 1.75 1.75v16.5A1.75 1.75 0 0 1 20.25 22H3.75A1.75 1.75 0 0 1 2 20.25Zm1.75-.25a.25.25 0 0 0-.25.25v16.5c0 .138.112.25.25.25h16.5a.25.25 0 0 0 .25-.25V3.75a.25.25 0 0 0-.25-.25Z"></path> </svg> <div> <div class="color-fg-default h4">Code Search</div> Find more, search less </div> </a></li> </ul> </div> </div> <div class="HeaderMenu-column px-lg-4"> <div class="border-bottom pb-3 pb-lg-0 border-lg-bottom-0 border-bottom-0"> <span class="d-block h4 color-fg-default my-1" id="product-explore-heading">Explore</span> <ul class="list-style-none f5" aria-labelledby="product-explore-heading"> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{"location":"navbar","action":"all_features","context":"product","tag":"link","label":"all_features_link_product_navbar"}" href="https://github.com/features"> All features </a></li> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative 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dir=\"auto\"\u003eread2tree\u003c/h1\u003e\u003ca id=\"user-content-read2tree\" class=\"anchor\" aria-label=\"Permalink: read2tree\" href=\"#read2tree\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eread2tree is a software tool that allows to obtain alignment matrices for tree inference. For this purpose it makes use of the OMA database and a set of reads. Its strength lies in the fact that it bipasses the several standard steps when obtaining such a matrix in regular analysis. These steps are read filtereing, assembly, gene prediction, gene annotation, all vs all comparison, orthology prediction, alignment and concatination.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eread2tree works in linux with \u003ca href=\"https://www.python.org/downloads/release/python-310/\" rel=\"nofollow\"\u003e\u003cimg src=\"https://camo.githubusercontent.com/04c1e31dfdb74802d1f343bff282418e554accd0fe2674d238a68cd12bd2fd44/68747470733a2f2f696d672e736869656c64732e696f2f62616467652f707974686f6e2d332e31302e382d626c75652e737667\" alt=\"Python 3.10.8\" data-canonical-src=\"https://img.shields.io/badge/python-3.10.8-blue.svg\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eImportant note\u003c/h2\u003e\u003ca id=\"user-content-important-note\" class=\"anchor\" aria-label=\"Permalink: Important note\" href=\"#important-note\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eIf you want to re-run a read2tree analysis (after facing an error, or changing the inputs), please make sure that you removed the \u003ccode\u003emplog.log\u003c/code\u003e file and the output folder. Alternatively you could start from an empty folder. Otherwise, read2tree might use the faulty output of previous unfinished run.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eWe are working on a new \u003ca href=\"https://github.com/DessimozLab/read2tree/tree/minimap2\"\u003eread2tree version\u003c/a\u003e using the \u003ca href=\"https://github.com/lh3/minimap2\"\u003eminimap2\u003c/a\u003e aligner, which is much faster. For this version, the \u003ccode\u003e--read_type\u003c/code\u003e argument could be either \u003ccode\u003eshort\u003c/code\u003e, \u003ccode\u003elong-hifi\u003c/code\u003e or \u003ccode\u003elong-ont\u003c/code\u003e. You could also use \u003ccode\u003e--threads 40\u003c/code\u003e to be used with minimap2.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eRead2Tree Talk:\u003c/h2\u003e\u003ca id=\"user-content-read2tree-talk\" class=\"anchor\" aria-label=\"Permalink: Read2Tree Talk:\" href=\"#read2tree-talk\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eYou can watch David Dylus's presentation on Read2Tree as part of the SIB \u003ca href=\"https://www.sib.swiss/in-silico-talks/read2tree-inferring-phylogenetic-trees-from-raw-sequencing-data\" rel=\"nofollow\"\u003ein silico talks\u003c/a\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eRead2Tree publication\u003c/h2\u003e\u003ca id=\"user-content-read2tree-publication\" class=\"anchor\" aria-label=\"Permalink: Read2Tree publication\" href=\"#read2tree-publication\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eYou can cite Read2Tree published in \u003ca href=\"https://doi.org/10.1038/s41587-023-01753-4\" rel=\"nofollow\"\u003eNature Biotechnology\u003c/a\u003e:\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"David Dylus, Adrian Altenhoff, Sina Majidian, Fritz J. Sedlazeck \u0026amp; Christophe Dessimoz.\n\nInference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01753-4/.\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003eDavid Dylus, Adrian Altenhoff, Sina Majidian, Fritz J. Sedlazeck \u0026amp; Christophe Dessimoz.\n\nInference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01753-4/.\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch1 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eInstallation\u003c/h1\u003e\u003ca id=\"user-content-installation\" class=\"anchor\" aria-label=\"Permalink: Installation\" href=\"#installation\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThere are three ways to install read2tree. You can choose either of them.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003e1) Installation from source\u003c/h3\u003e\u003ca id=\"user-content-1-installation-from-source\" class=\"anchor\" aria-label=\"Permalink: 1) Installation from source\" href=\"#1-installation-from-source\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eTo set up read2tree on your local machine from source please follow the instructions below.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eFirst, we need to create a fresh \u003ca href=\"https://docs.conda.io/en/latest/miniconda.html\" rel=\"nofollow\"\u003econda\u003c/a\u003e environment:\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"conda create -n r2t python=3.10.8\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003econda create -n r2t python=3.10.8\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch4 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003ePrerequisites\u003c/h4\u003e\u003ca id=\"user-content-prerequisites\" class=\"anchor\" aria-label=\"Permalink: Prerequisites\" href=\"#prerequisites\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe following python packages are needed: \u003ca href=\"https://github.com/numpy/numpy\"\u003enumpy\u003c/a\u003e, \u003ca href=\"https://github.com/scipy/scipy\"\u003escipy\u003c/a\u003e, \u003ca href=\"https://github.com/cython/cython\"\u003ecython\u003c/a\u003e, \u003ca href=\"https://github.com/lxml/lxml\"\u003elxml\u003c/a\u003e, \u003ca href=\"https://tqdm.github.io/docs/tqdm\" rel=\"nofollow\"\u003etqdm\u003c/a\u003e, \u003ca href=\"https://github.com/pysam-developers/pysam\"\u003epysam\u003c/a\u003e, \u003ca href=\"https://svn.code.sf.net/p/pyparsing/code/\" rel=\"nofollow\"\u003epyparsing\u003c/a\u003e, \u003ca href=\"http://python-requests.org\" rel=\"nofollow\"\u003erequests\u003c/a\u003e, \u003ca href=\"https://github.com/benediktschmitt/py-filelock\"\u003efilelock\u003c/a\u003e, \u003ca href=\"https://github.com/SethMMorton/natsort\"\u003enatsort\u003c/a\u003e, \u003ca href=\"http://pyyaml.org/wiki/PyYAML\" rel=\"nofollow\"\u003epyyaml\u003c/a\u003e, \u003ca href=\"https://github.com/biopython/biopython\"\u003ebiopython\u003c/a\u003e, \u003ca href=\"http://etetoolkit.org\" rel=\"nofollow\"\u003eete3\u003c/a\u003e, \u003ca href=\"http://packages.python.org/DendroPy/\" rel=\"nofollow\"\u003edendropy\u003c/a\u003e.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eYou can install all of them using.\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"conda install -c conda-forge biopython numpy Cython ete3 lxml tqdm scipy pyparsing requests natsort pyyaml filelock\nconda install -c bioconda dendropy pysam\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003econda install -c conda-forge biopython numpy Cython ete3 lxml tqdm scipy pyparsing requests natsort pyyaml filelock\nconda install -c bioconda dendropy pysam\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eBesides, you need softwares including \u003ca href=\"http://mafft.cbrc.jp/alignment/software/\" rel=\"nofollow\"\u003emafft\u003c/a\u003e (multiple sequence aligner), \u003ca href=\"http://www.iqtree.org/\" rel=\"nofollow\"\u003eiqtree\u003c/a\u003e (phylogenomic inference), \u003ca href=\"https://github.com/philres/ngmlr\"\u003engmlr\u003c/a\u003e, \u003ca href=\"https://github.com/Cibiv/NextGenMap\"\u003engm/nextgenmap\u003c/a\u003e (long and short read mappers), and \u003ca href=\"http://www.htslib.org/download/\" rel=\"nofollow\"\u003esamtools\u003c/a\u003e which could be installed using conda.\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"conda install -c bioconda mafft iqtree ngmlr nextgenmap samtools\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003econda install -c bioconda mafft iqtree ngmlr nextgenmap samtools\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThen, you can install the read2tree package after downlaoding the package from this GitHub repo using\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"git clone https://github.com/DessimozLab/read2tree.git\ncd read2tree\npython setup.py install\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003egit clone https://github.com/DessimozLab/read2tree.git\ncd read2tree\npython setup.py install\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003e2) Installation using Conda\u003c/h3\u003e\u003ca id=\"user-content-2-installation-using-conda\" class=\"anchor\" aria-label=\"Permalink: 2) Installation using Conda\" href=\"#2-installation-using-conda\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"conda create -n r2t python=3.10.8\nconda install -c bioconda read2tree \n\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003econda create -n r2t python=3.10.8\nconda install -c bioconda read2tree \n\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eAlternatively, you could also try using \u003ca href=\"https://mamba.readthedocs.io/en/latest/\" rel=\"nofollow\"\u003emamba\u003c/a\u003e. Caution: please read about compatiblity of conda and mamba in one envirnoment.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003e3) Installation using Docker\u003c/h3\u003e\u003ca id=\"user-content-3-installation-using-docker\" class=\"anchor\" aria-label=\"Permalink: 3) Installation using Docker\" href=\"#3-installation-using-docker\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe Dockerfile is also available in this repository. There is an example how to run in the \u003ca href=\"#test-example\"\u003etest example\u003c/a\u003e section.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eA prebuild container can be loaded from dockerhub:\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"docker pull dessimozlab/read2tree:latest\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003edocker pull dessimozlab/read2tree:latest\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eRun\u003c/h2\u003e\u003ca id=\"user-content-run\" class=\"anchor\" aria-label=\"Permalink: Run\" href=\"#run\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eTo run read2tree two things are required as input:\u003c/p\u003e\n\u003col dir=\"auto\"\u003e\n\u003cli\u003eThe DNA sequencing reads as FASTQ file(s).\u003c/li\u003e\n\u003cli\u003eA set of reference orthologous groups, i.e. marker genes.\nIn our wiki \u003ca href=\"https://github.com/DessimozLab/read2tree/wiki/obtaining-marker-genes\"\u003epage\u003c/a\u003e, you may find information on how to obtain the marker genes using \u003ca href=\"https://omabrowser.org/oma/export_markers\" rel=\"nofollow\"\u003eOMA browser\u003c/a\u003e. You can set the value of \u003ccode\u003eMaximum nr of markers\u003c/code\u003e as 200 or 400. Once you downloaded the tgz file, run this\u003c/li\u003e\n\u003c/ol\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"tar xvzf marker_genes_*.tgz \nls marker_genes/*.fna | wc -l\ncat marker_genes/*.fna \u0026gt; dna_ref.fa\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003etar xvzf marker_genes_*.tgz \nls marker_genes/*.fna | wc -l\ncat marker_genes/*.fna \u0026gt; dna_ref.fa\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eoutput\u003c/h3\u003e\u003ca id=\"user-content-output\" class=\"anchor\" aria-label=\"Permalink: output\" href=\"#output\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe output of Read2Tree is the concatenated alignments as a fasta file where each record corresponds to one species. We also provide the option \u003ccode\u003e--tree\u003c/code\u003e for inferring the species tree using IQTREE as defualt.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eSingle species mode\u003c/h3\u003e\u003ca id=\"user-content-single-species-mode\" class=\"anchor\" aria-label=\"Permalink: Single species mode\" href=\"#single-species-mode\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"read2tree --tree --standalone_path marker_genes/ --reads read_1.fastq read_2.fastq --output_path output --dna_reference dna_ref.fa \"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003eread2tree --tree --standalone_path marker_genes/ --reads read_1.fastq read_2.fastq --output_path output --dna_reference dna_ref.fa \n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eMultiple species mode\u003c/h3\u003e\u003ca id=\"user-content-multiple-species-mode\" class=\"anchor\" aria-label=\"Permalink: Multiple species mode\" href=\"#multiple-species-mode\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"read2tree --standalone_path marker_genes/ --output_path output --reference --dna_reference dna_ref.fa # this creates just the reference folder 01 - 03\nread2tree --standalone_path marker_genes/ --output_path output --reads species1_R1.fastq species2_R2.fastq\nread2tree --standalone_path marker_genes/ --output_path output --reads species2_R1.fastq species2_R2.fastq\nread2tree --standalone_path marker_genes/ --output_path output --reads species3_R1.fastq species3_R2.fastq\nread2tree --standalone_path marker_genes/ --output_path output --merge_all_mappings --tree\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003eread2tree --standalone_path marker_genes/ --output_path output --reference --dna_reference dna_ref.fa # this creates just the reference folder 01 - 03\nread2tree --standalone_path marker_genes/ --output_path output --reads species1_R1.fastq species2_R2.fastq\nread2tree --standalone_path marker_genes/ --output_path output --reads species2_R1.fastq species2_R2.fastq\nread2tree --standalone_path marker_genes/ --output_path output --reads species3_R1.fastq species3_R2.fastq\nread2tree --standalone_path marker_genes/ --output_path output --merge_all_mappings --tree\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003ebootstraping\u003c/h3\u003e\u003ca id=\"user-content-bootstraping\" class=\"anchor\" aria-label=\"Permalink: bootstraping\" href=\"#bootstraping\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eTo have bootstrap values a metric for quality of internal nodes, you can run the following\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"thread=20\niqtree -T ${thread} -s output/concat_*_aa.phy -bb 1000 \"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003ethread=20\niqtree -T ${thread} -s output/concat_*_aa.phy -bb 1000 \n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe \u003ccode\u003e.phy\u003c/code\u003e file is either \u003ccode\u003econcat_sample_aa.phy\u003c/code\u003e or \u003ccode\u003econcat_merge_aa.phy\u003c/code\u003e corresponding to single- or multi-species mode.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eIt is also possible to use \u003ca href=\"http://trimal.cgenomics.org/use_of_the_command_line_trimal_v1.2\" rel=\"nofollow\"\u003etrimal\u003c/a\u003e for trimming msa \u003ccode\u003etrimal -in \u0026lt;inputfile\u0026gt; -out \u0026lt;outputfile\u0026gt; -automated1\u003c/code\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eDNA-mode tree inference\u003c/h3\u003e\u003ca id=\"user-content-dna-mode-tree-inference\" class=\"anchor\" aria-label=\"Permalink: DNA-mode tree inference\" href=\"#dna-mode-tree-inference\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eFor closely related species, the user can infer tree using MSA of nucleotide sequences.\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"thread=20\niqtree -T ${thread} -s output/concat_*_dna.phy \"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003ethread=20\niqtree -T ${thread} -s output/concat_*_dna.phy \n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eTest example\u003c/h2\u003e\u003ca id=\"user-content-test-example\" class=\"anchor\" aria-label=\"Permalink: Test example\" href=\"#test-example\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe goal of this test example is to infer species tree for Mus musculus using its sequencing reads. You can download the full read data from from \u003ca href=\"https://www.ncbi.nlm.nih.gov/sra/?term=SRR5171076\" rel=\"nofollow\"\u003eSRR5171076\u003c/a\u003e using \u003ca href=\"https://anaconda.org/bioconda/sra-tools\" rel=\"nofollow\"\u003esra-tools\u003c/a\u003e. Alternatively, a small read dataset is provided in the \u003ccode\u003etests\u003c/code\u003e folder. For this example, we consider five species including Mnemiopsis leidyi, Xenopus laevis, Homo sapiens, Gorilla gorilla, and Rattus norvegicus as the reference. Using \u003ca href=\"https://omabrowser.org/oma/export_markers\" rel=\"nofollow\"\u003eOMA browser\u003c/a\u003e, we downloaded 20 marker genes of these five species as the reference orthologous groups, located in the folder \u003ccode\u003etests/mareker_genes\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"cd tests\nread2tree --debug --tree --standalone_path marker_genes/ --reads sample_1.fastq sample_2.fastq --output_path output/ --dna_reference dna_ref.fa \"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003ecd tests\nread2tree --debug --tree --standalone_path marker_genes/ --reads sample_1.fastq sample_2.fastq --output_path output/ --dna_reference dna_ref.fa \n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch4 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eRun test example using docker\u003c/h4\u003e\u003ca id=\"user-content-run-test-example-using-docker\" class=\"anchor\" aria-label=\"Permalink: Run test example using docker\" href=\"#run-test-example-using-docker\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"docker run --rm -i -v $PWD/tests:/input -v $PWD/tests/:/reads -v $PWD/output:/out -v $PWD/run:/run dessimozlab/read2tree:latest --tree --standalone_path /input/marker_genes --dna_reference /input/cds-marker_genes.fasta.gz --reads /reads/sample_1.fastq --output_path /out\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003edocker run --rm -i -v $PWD/tests:/input -v $PWD/tests/:/reads -v $PWD/output:/out -v $PWD/run:/run dessimozlab/read2tree:latest --tree --standalone_path /input/marker_genes --dna_reference /input/cds-marker_genes.fasta.gz --reads /reads/sample_1.fastq --output_path /out\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eoutput files\u003c/h3\u003e\u003ca id=\"user-content-output-files\" class=\"anchor\" aria-label=\"Permalink: output files\" href=\"#output-files\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eYou can check the inferred species tree for the sample and five reference species in Newick format:\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"$cat output/tree_sample_1.nwk\n(sample_1:0.0106979811,((HUMAN:0.0041202790,GORGO:0.0272785216):0.0433094119,(XENLA:0.1715052824,MNELE:0.9177670816):0.1141311779):0.0613339433,RATNO:0.0123413734);\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003e$cat output/tree_sample_1.nwk\n(sample_1:0.0106979811,((HUMAN:0.0041202790,GORGO:0.0272785216):0.0433094119,(XENLA:0.1715052824,MNELE:0.9177670816):0.1141311779):0.0613339433,RATNO:0.0123413734);\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eFor the full description of output files please check our wiki \u003ca href=\"https://github.com/DessimozLab/read2tree/wiki/output-files\"\u003epage\u003c/a\u003e.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eNote that we consider species names as 5-letter codes e.g. XENLA = Xenopus laevis. If you want to rerun your analysis, make sure that you moved/deleted the files. Otherwise, read2tree continues the progress of previous analysis.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eFor running on clusters, you can run the first step of read2tree such that folders 01, 02 and 03 are computed (this allows for mapping). This can be done using the '--reference' option. Since read2tree re-orders the OGs into the included species, it is possible to split the mapping step per species using multiple threads for the mapper. For this the '--single_mapping' option is available.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eHint: As read2tree exploits the \u003ccode\u003eprogress\u003c/code\u003e package, the user can benefit from continuing unfinished runs. However, if you want to conduct a new analysis with different inputs, you need to remove output of previous runs or change the \u003ccode\u003eoutput_path\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eDetails of arguments\u003c/h3\u003e\u003ca id=\"user-content-details-of-arguments\" class=\"anchor\" aria-label=\"Permalink: Details of arguments\" href=\"#details-of-arguments\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eTo see the details of arguments, please take look at our wiki \u003ca href=\"https://github.com/DessimozLab/read2tree/wiki/Details-of-arguments\"\u003epage\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003ePossible issues\u003c/h2\u003e\u003ca id=\"user-content-possible-issues\" class=\"anchor\" aria-label=\"Permalink: Possible issues\" href=\"#possible-issues\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eInstalling on MAC sometimes drops this error:\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"raise ValueError, 'unknown locale: %s' % localename\nValueError: unknown locale: UTF-8\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003eraise ValueError, 'unknown locale: %s' % localename\nValueError: unknown locale: UTF-8\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThis can be mitigated using:\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"export LC_ALL=en_US.UTF-8\nexport LANG=en_US.UTF-8\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003eexport LC_ALL=en_US.UTF-8\nexport LANG=en_US.UTF-8\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eChange log\u003c/h2\u003e\u003ca id=\"user-content-change-log\" class=\"anchor\" aria-label=\"Permalink: Change log\" href=\"#change-log\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\n\u003cp dir=\"auto\"\u003eversion 0.1.5:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003efix issue with UnknownSeq being removed in Biopython\u0026gt;1.80\u003c/li\u003e\n\u003cli\u003eremoving unused modeltester wrappers\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp dir=\"auto\"\u003eversion 0.1.4:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003eallow reference folders not named marker_genes (#12)\u003c/li\u003e\n\u003cli\u003eupdate environment.yml file to contain all dependencies (#16)\u003c/li\u003e\n\u003cli\u003edocumentation improvements\u003c/li\u003e\n\u003cli\u003eCI/CD pipeline\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp dir=\"auto\"\u003eversion 0.1.3:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003eimprovements of documentation\u003c/li\u003e\n\u003cli\u003eadding support for docker\u003c/li\u003e\n\u003cli\u003esmall bugfixes\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp dir=\"auto\"\u003eversion 0.1.2: packaging\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp dir=\"auto\"\u003eversion 0.1.0: Adding covid analysis\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp dir=\"auto\"\u003eversion 0.0: Initial work\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eAuthors\u003c/h2\u003e\u003ca id=\"user-content-authors\" class=\"anchor\" aria-label=\"Permalink: Authors\" href=\"#authors\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/dvdylus\"\u003eDavid Dylus\u003c/a\u003e, (main author)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://people.inf.ethz.ch/adriaal\" rel=\"nofollow\"\u003eAdrian Altenhoff\u003c/a\u003e.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp dir=\"auto\"\u003eThe authors would like to thank Alex Warwick for help how to initiate such a package.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eLicense\u003c/h2\u003e\u003ca id=\"user-content-license\" class=\"anchor\" aria-label=\"Permalink: License\" href=\"#license\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThis project is licensed under the MIT License.\u003c/p\u003e\n\u003c/article\u003e","loaded":true,"timedOut":false,"errorMessage":null,"headerInfo":{"toc":[{"level":1,"text":"read2tree","anchor":"read2tree","htmlText":"read2tree"},{"level":2,"text":"Important note","anchor":"important-note","htmlText":"Important note"},{"level":2,"text":"Read2Tree Talk:","anchor":"read2tree-talk","htmlText":"Read2Tree Talk:"},{"level":2,"text":"Read2Tree publication","anchor":"read2tree-publication","htmlText":"Read2Tree publication"},{"level":1,"text":"Installation","anchor":"installation","htmlText":"Installation"},{"level":3,"text":"1) Installation from source","anchor":"1-installation-from-source","htmlText":"1) Installation from source"},{"level":4,"text":"Prerequisites","anchor":"prerequisites","htmlText":"Prerequisites"},{"level":3,"text":"2) Installation using Conda","anchor":"2-installation-using-conda","htmlText":"2) Installation using Conda"},{"level":3,"text":"3) Installation using Docker","anchor":"3-installation-using-docker","htmlText":"3) Installation using Docker"},{"level":2,"text":"Run","anchor":"run","htmlText":"Run"},{"level":3,"text":"output","anchor":"output","htmlText":"output"},{"level":3,"text":"Single species mode","anchor":"single-species-mode","htmlText":"Single species mode"},{"level":3,"text":"Multiple species mode","anchor":"multiple-species-mode","htmlText":"Multiple species mode"},{"level":3,"text":"bootstraping","anchor":"bootstraping","htmlText":"bootstraping"},{"level":3,"text":"DNA-mode tree inference","anchor":"dna-mode-tree-inference","htmlText":"DNA-mode tree inference"},{"level":2,"text":"Test example","anchor":"test-example","htmlText":"Test example"},{"level":4,"text":"Run test example using docker","anchor":"run-test-example-using-docker","htmlText":"Run test example using docker"},{"level":3,"text":"output files","anchor":"output-files","htmlText":"output files"},{"level":3,"text":"Details of arguments","anchor":"details-of-arguments","htmlText":"Details of arguments"},{"level":2,"text":"Possible issues","anchor":"possible-issues","htmlText":"Possible issues"},{"level":2,"text":"Change log","anchor":"change-log","htmlText":"Change 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0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">read2tree is a software tool that allows to obtain alignment matrices for tree inference. For this purpose it makes use of the OMA database and a set of reads. Its strength lies in the fact that it bipasses the several standard steps when obtaining such a matrix in regular analysis. These steps are read filtereing, assembly, gene prediction, gene annotation, all vs all comparison, orthology prediction, alignment and concatination.</p> <p dir="auto">read2tree works in linux with <a href="https://www.python.org/downloads/release/python-310/" rel="nofollow"><img src="https://camo.githubusercontent.com/04c1e31dfdb74802d1f343bff282418e554accd0fe2674d238a68cd12bd2fd44/68747470733a2f2f696d672e736869656c64732e696f2f62616467652f707974686f6e2d332e31302e382d626c75652e737667" alt="Python 3.10.8" data-canonical-src="https://img.shields.io/badge/python-3.10.8-blue.svg" style="max-width: 100%;"></a></p> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Important note</h2><a id="user-content-important-note" class="anchor" aria-label="Permalink: Important note" href="#important-note"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">If you want to re-run a read2tree analysis (after facing an error, or changing the inputs), please make sure that you removed the <code>mplog.log</code> file and the output folder. Alternatively you could start from an empty folder. Otherwise, read2tree might use the faulty output of previous unfinished run.</p> <p dir="auto">We are working on a new <a href="https://github.com/DessimozLab/read2tree/tree/minimap2">read2tree version</a> using the <a href="https://github.com/lh3/minimap2">minimap2</a> aligner, which is much faster. For this version, the <code>--read_type</code> argument could be either <code>short</code>, <code>long-hifi</code> or <code>long-ont</code>. You could also use <code>--threads 40</code> to be used with minimap2.</p> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Read2Tree Talk:</h2><a id="user-content-read2tree-talk" class="anchor" aria-label="Permalink: Read2Tree Talk:" href="#read2tree-talk"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">You can watch David Dylus's presentation on Read2Tree as part of the SIB <a href="https://www.sib.swiss/in-silico-talks/read2tree-inferring-phylogenetic-trees-from-raw-sequencing-data" rel="nofollow">in silico talks</a>.</p> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Read2Tree publication</h2><a id="user-content-read2tree-publication" class="anchor" aria-label="Permalink: Read2Tree publication" href="#read2tree-publication"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">You can cite Read2Tree published in <a href="https://doi.org/10.1038/s41587-023-01753-4" rel="nofollow">Nature Biotechnology</a>:</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="David Dylus, Adrian Altenhoff, Sina Majidian, Fritz J. Sedlazeck & Christophe Dessimoz. Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01753-4/."><pre class="notranslate"><code>David Dylus, Adrian Altenhoff, Sina Majidian, Fritz J. Sedlazeck & Christophe Dessimoz. Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01753-4/. </code></pre></div> <div class="markdown-heading" dir="auto"><h1 tabindex="-1" class="heading-element" dir="auto">Installation</h1><a id="user-content-installation" class="anchor" aria-label="Permalink: Installation" href="#installation"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">There are three ways to install read2tree. You can choose either of them.</p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">1) Installation from source</h3><a id="user-content-1-installation-from-source" class="anchor" aria-label="Permalink: 1) Installation from source" href="#1-installation-from-source"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">To set up read2tree on your local machine from source please follow the instructions below.</p> <p dir="auto">First, we need to create a fresh <a href="https://docs.conda.io/en/latest/miniconda.html" rel="nofollow">conda</a> environment:</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="conda create -n r2t python=3.10.8"><pre class="notranslate"><code>conda create -n r2t python=3.10.8 </code></pre></div> <div class="markdown-heading" dir="auto"><h4 tabindex="-1" class="heading-element" dir="auto">Prerequisites</h4><a id="user-content-prerequisites" class="anchor" aria-label="Permalink: Prerequisites" href="#prerequisites"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">The following python packages are needed: <a href="https://github.com/numpy/numpy">numpy</a>, <a href="https://github.com/scipy/scipy">scipy</a>, <a href="https://github.com/cython/cython">cython</a>, <a href="https://github.com/lxml/lxml">lxml</a>, <a href="https://tqdm.github.io/docs/tqdm" rel="nofollow">tqdm</a>, <a href="https://github.com/pysam-developers/pysam">pysam</a>, <a href="https://svn.code.sf.net/p/pyparsing/code/" rel="nofollow">pyparsing</a>, <a href="http://python-requests.org" rel="nofollow">requests</a>, <a href="https://github.com/benediktschmitt/py-filelock">filelock</a>, <a href="https://github.com/SethMMorton/natsort">natsort</a>, <a href="http://pyyaml.org/wiki/PyYAML" rel="nofollow">pyyaml</a>, <a href="https://github.com/biopython/biopython">biopython</a>, <a href="http://etetoolkit.org" rel="nofollow">ete3</a>, <a href="http://packages.python.org/DendroPy/" rel="nofollow">dendropy</a>.</p> <p dir="auto">You can install all of them using.</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="conda install -c conda-forge biopython numpy Cython ete3 lxml tqdm scipy pyparsing requests natsort pyyaml filelock conda install -c bioconda dendropy pysam"><pre class="notranslate"><code>conda install -c conda-forge biopython numpy Cython ete3 lxml tqdm scipy pyparsing requests natsort pyyaml filelock conda install -c bioconda dendropy pysam </code></pre></div> <p dir="auto">Besides, you need softwares including <a href="http://mafft.cbrc.jp/alignment/software/" rel="nofollow">mafft</a> (multiple sequence aligner), <a href="http://www.iqtree.org/" rel="nofollow">iqtree</a> (phylogenomic inference), <a href="https://github.com/philres/ngmlr">ngmlr</a>, <a href="https://github.com/Cibiv/NextGenMap">ngm/nextgenmap</a> (long and short read mappers), and <a href="http://www.htslib.org/download/" rel="nofollow">samtools</a> which could be installed using conda.</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="conda install -c bioconda mafft iqtree ngmlr nextgenmap samtools"><pre class="notranslate"><code>conda install -c bioconda mafft iqtree ngmlr nextgenmap samtools </code></pre></div> <p dir="auto">Then, you can install the read2tree package after downlaoding the package from this GitHub repo using</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="git clone https://github.com/DessimozLab/read2tree.git cd read2tree python setup.py install"><pre class="notranslate"><code>git clone https://github.com/DessimozLab/read2tree.git cd read2tree python setup.py install </code></pre></div> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">2) Installation using Conda</h3><a id="user-content-2-installation-using-conda" class="anchor" aria-label="Permalink: 2) Installation using Conda" href="#2-installation-using-conda"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="conda create -n r2t python=3.10.8 conda install -c bioconda read2tree "><pre class="notranslate"><code>conda create -n r2t python=3.10.8 conda install -c bioconda read2tree </code></pre></div> <p dir="auto">Alternatively, you could also try using <a href="https://mamba.readthedocs.io/en/latest/" rel="nofollow">mamba</a>. Caution: please read about compatiblity of conda and mamba in one envirnoment.</p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">3) Installation using Docker</h3><a id="user-content-3-installation-using-docker" class="anchor" aria-label="Permalink: 3) Installation using Docker" href="#3-installation-using-docker"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">The Dockerfile is also available in this repository. There is an example how to run in the <a href="#test-example">test example</a> section.</p> <p dir="auto">A prebuild container can be loaded from dockerhub:</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="docker pull dessimozlab/read2tree:latest"><pre class="notranslate"><code>docker pull dessimozlab/read2tree:latest </code></pre></div> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Run</h2><a id="user-content-run" class="anchor" aria-label="Permalink: Run" href="#run"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">To run read2tree two things are required as input:</p> <ol dir="auto"> <li>The DNA sequencing reads as FASTQ file(s).</li> <li>A set of reference orthologous groups, i.e. marker genes. In our wiki <a href="https://github.com/DessimozLab/read2tree/wiki/obtaining-marker-genes">page</a>, you may find information on how to obtain the marker genes using <a href="https://omabrowser.org/oma/export_markers" rel="nofollow">OMA browser</a>. You can set the value of <code>Maximum nr of markers</code> as 200 or 400. Once you downloaded the tgz file, run this</li> </ol> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="tar xvzf marker_genes_*.tgz ls marker_genes/*.fna | wc -l cat marker_genes/*.fna > dna_ref.fa"><pre class="notranslate"><code>tar xvzf marker_genes_*.tgz ls marker_genes/*.fna | wc -l cat marker_genes/*.fna > dna_ref.fa </code></pre></div> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">output</h3><a id="user-content-output" class="anchor" aria-label="Permalink: output" href="#output"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">The output of Read2Tree is the concatenated alignments as a fasta file where each record corresponds to one species. We also provide the option <code>--tree</code> for inferring the species tree using IQTREE as defualt.</p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Single species mode</h3><a id="user-content-single-species-mode" class="anchor" aria-label="Permalink: Single species mode" href="#single-species-mode"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="read2tree --tree --standalone_path marker_genes/ --reads read_1.fastq read_2.fastq --output_path output --dna_reference dna_ref.fa "><pre class="notranslate"><code>read2tree --tree --standalone_path marker_genes/ --reads read_1.fastq read_2.fastq --output_path output --dna_reference dna_ref.fa </code></pre></div> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Multiple species mode</h3><a id="user-content-multiple-species-mode" class="anchor" aria-label="Permalink: Multiple species mode" href="#multiple-species-mode"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="read2tree --standalone_path marker_genes/ --output_path output --reference --dna_reference dna_ref.fa # this creates just the reference folder 01 - 03 read2tree --standalone_path marker_genes/ --output_path output --reads species1_R1.fastq species2_R2.fastq read2tree --standalone_path marker_genes/ --output_path output --reads species2_R1.fastq species2_R2.fastq read2tree --standalone_path marker_genes/ --output_path output --reads species3_R1.fastq species3_R2.fastq read2tree --standalone_path marker_genes/ --output_path output --merge_all_mappings --tree"><pre class="notranslate"><code>read2tree --standalone_path marker_genes/ --output_path output --reference --dna_reference dna_ref.fa # this creates just the reference folder 01 - 03 read2tree --standalone_path marker_genes/ --output_path output --reads species1_R1.fastq species2_R2.fastq read2tree --standalone_path marker_genes/ --output_path output --reads species2_R1.fastq species2_R2.fastq read2tree --standalone_path marker_genes/ --output_path output --reads species3_R1.fastq species3_R2.fastq read2tree --standalone_path marker_genes/ --output_path output --merge_all_mappings --tree </code></pre></div> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">bootstraping</h3><a id="user-content-bootstraping" class="anchor" aria-label="Permalink: bootstraping" href="#bootstraping"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">To have bootstrap values a metric for quality of internal nodes, you can run the following</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="thread=20 iqtree -T ${thread} -s output/concat_*_aa.phy -bb 1000 "><pre class="notranslate"><code>thread=20 iqtree -T ${thread} -s output/concat_*_aa.phy -bb 1000 </code></pre></div> <p dir="auto">The <code>.phy</code> file is either <code>concat_sample_aa.phy</code> or <code>concat_merge_aa.phy</code> corresponding to single- or multi-species mode.</p> <p dir="auto">It is also possible to use <a href="http://trimal.cgenomics.org/use_of_the_command_line_trimal_v1.2" rel="nofollow">trimal</a> for trimming msa <code>trimal -in <inputfile> -out <outputfile> -automated1</code></p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">DNA-mode tree inference</h3><a id="user-content-dna-mode-tree-inference" class="anchor" aria-label="Permalink: DNA-mode tree inference" href="#dna-mode-tree-inference"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">For closely related species, the user can infer tree using MSA of nucleotide sequences.</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="thread=20 iqtree -T ${thread} -s output/concat_*_dna.phy "><pre class="notranslate"><code>thread=20 iqtree -T ${thread} -s output/concat_*_dna.phy </code></pre></div> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Test example</h2><a id="user-content-test-example" class="anchor" aria-label="Permalink: Test example" href="#test-example"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">The goal of this test example is to infer species tree for Mus musculus using its sequencing reads. You can download the full read data from from <a href="https://www.ncbi.nlm.nih.gov/sra/?term=SRR5171076" rel="nofollow">SRR5171076</a> using <a href="https://anaconda.org/bioconda/sra-tools" rel="nofollow">sra-tools</a>. Alternatively, a small read dataset is provided in the <code>tests</code> folder. For this example, we consider five species including Mnemiopsis leidyi, Xenopus laevis, Homo sapiens, Gorilla gorilla, and Rattus norvegicus as the reference. Using <a href="https://omabrowser.org/oma/export_markers" rel="nofollow">OMA browser</a>, we downloaded 20 marker genes of these five species as the reference orthologous groups, located in the folder <code>tests/mareker_genes</code>.</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="cd tests read2tree --debug --tree --standalone_path marker_genes/ --reads sample_1.fastq sample_2.fastq --output_path output/ --dna_reference dna_ref.fa "><pre class="notranslate"><code>cd tests read2tree --debug --tree --standalone_path marker_genes/ --reads sample_1.fastq sample_2.fastq --output_path output/ --dna_reference dna_ref.fa </code></pre></div> <div class="markdown-heading" dir="auto"><h4 tabindex="-1" class="heading-element" dir="auto">Run test example using docker</h4><a id="user-content-run-test-example-using-docker" class="anchor" aria-label="Permalink: Run test example using docker" href="#run-test-example-using-docker"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="docker run --rm -i -v $PWD/tests:/input -v $PWD/tests/:/reads -v $PWD/output:/out -v $PWD/run:/run dessimozlab/read2tree:latest --tree --standalone_path /input/marker_genes --dna_reference /input/cds-marker_genes.fasta.gz --reads /reads/sample_1.fastq --output_path /out"><pre class="notranslate"><code>docker run --rm -i -v $PWD/tests:/input -v $PWD/tests/:/reads -v $PWD/output:/out -v $PWD/run:/run dessimozlab/read2tree:latest --tree --standalone_path /input/marker_genes --dna_reference /input/cds-marker_genes.fasta.gz --reads /reads/sample_1.fastq --output_path /out </code></pre></div> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">output files</h3><a id="user-content-output-files" class="anchor" aria-label="Permalink: output files" href="#output-files"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">You can check the inferred species tree for the sample and five reference species in Newick format:</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="$cat output/tree_sample_1.nwk (sample_1:0.0106979811,((HUMAN:0.0041202790,GORGO:0.0272785216):0.0433094119,(XENLA:0.1715052824,MNELE:0.9177670816):0.1141311779):0.0613339433,RATNO:0.0123413734);"><pre class="notranslate"><code>$cat output/tree_sample_1.nwk (sample_1:0.0106979811,((HUMAN:0.0041202790,GORGO:0.0272785216):0.0433094119,(XENLA:0.1715052824,MNELE:0.9177670816):0.1141311779):0.0613339433,RATNO:0.0123413734); </code></pre></div> <p dir="auto">For the full description of output files please check our wiki <a href="https://github.com/DessimozLab/read2tree/wiki/output-files">page</a>.</p> <p dir="auto">Note that we consider species names as 5-letter codes e.g. XENLA = Xenopus laevis. If you want to rerun your analysis, make sure that you moved/deleted the files. Otherwise, read2tree continues the progress of previous analysis.</p> <p dir="auto">For running on clusters, you can run the first step of read2tree such that folders 01, 02 and 03 are computed (this allows for mapping). This can be done using the '--reference' option. Since read2tree re-orders the OGs into the included species, it is possible to split the mapping step per species using multiple threads for the mapper. For this the '--single_mapping' option is available.</p> <p dir="auto">Hint: As read2tree exploits the <code>progress</code> package, the user can benefit from continuing unfinished runs. However, if you want to conduct a new analysis with different inputs, you need to remove output of previous runs or change the <code>output_path</code>.</p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Details of arguments</h3><a id="user-content-details-of-arguments" class="anchor" aria-label="Permalink: Details of arguments" href="#details-of-arguments"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">To see the details of arguments, please take look at our wiki <a href="https://github.com/DessimozLab/read2tree/wiki/Details-of-arguments">page</a></p> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Possible issues</h2><a id="user-content-possible-issues" class="anchor" aria-label="Permalink: Possible issues" href="#possible-issues"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">Installing on MAC sometimes drops this error:</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="raise ValueError, 'unknown locale: %s' % localename ValueError: unknown locale: UTF-8"><pre class="notranslate"><code>raise ValueError, 'unknown locale: %s' % localename ValueError: unknown locale: UTF-8 </code></pre></div> <p dir="auto">This can be mitigated using:</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="export LC_ALL=en_US.UTF-8 export LANG=en_US.UTF-8"><pre class="notranslate"><code>export LC_ALL=en_US.UTF-8 export LANG=en_US.UTF-8 </code></pre></div> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Change log</h2><a id="user-content-change-log" class="anchor" aria-label="Permalink: Change log" href="#change-log"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <ul dir="auto"> <li> <p dir="auto">version 0.1.5:</p> <ul dir="auto"> <li>fix issue with UnknownSeq being removed in Biopython>1.80</li> <li>removing unused modeltester wrappers</li> </ul> </li> <li> <p dir="auto">version 0.1.4:</p> <ul dir="auto"> <li>allow reference folders not named marker_genes (#12)</li> <li>update environment.yml file to contain all dependencies (#16)</li> <li>documentation improvements</li> <li>CI/CD pipeline</li> </ul> </li> <li> <p dir="auto">version 0.1.3:</p> <ul dir="auto"> <li>improvements of documentation</li> <li>adding support for docker</li> <li>small bugfixes</li> </ul> </li> <li> <p dir="auto">version 0.1.2: packaging</p> </li> <li> <p dir="auto">version 0.1.0: Adding covid analysis</p> </li> <li> <p dir="auto">version 0.0: Initial work</p> </li> </ul> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Authors</h2><a id="user-content-authors" class="anchor" aria-label="Permalink: Authors" href="#authors"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <ul dir="auto"> <li><a href="https://github.com/dvdylus">David Dylus</a>, (main author)</li> <li><a href="http://people.inf.ethz.ch/adriaal" rel="nofollow">Adrian Altenhoff</a>.</li> </ul> <p dir="auto">The authors would like to thank Alex Warwick for help how to initiate such a package.</p> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">License</h2><a id="user-content-license" class="anchor" aria-label="Permalink: License" href="#license"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">This project is licensed under the MIT License.</p> </article></div></div></div></div></div> <!-- --> <!-- --> <script type="application/json" id="__PRIMER_DATA_:R0:__">{"resolvedServerColorMode":"day"}</script></div> </react-partial> <input type="hidden" data-csrf="true" value="PVYkrMPhAYNNBXJO9gmlFmzK8JjhqsV0JqkJ5jUEzi3Y0h8KPmELM5SvJrC+Fdnv0K7PRDsjAJzsAeMKyQH7+A==" /> </div> <div 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1.275.326.749.749 0 0 1-.215.734L9.06 8l3.22 3.22a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L8 9.06l-3.22 3.22a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042L6.94 8 3.72 4.78a.75.75 0 0 1 0-1.06Z"></path> </svg> </button> <div class="octocat-spinner my-6 js-details-dialog-spinner"></div> </details-dialog> </details> </template> <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;"> <div class="Popover-message Popover-message--bottom-left Popover-message--large Box color-shadow-large" style="width:360px;"> </div> </div> <template id="snippet-clipboard-copy-button"> <div class="zeroclipboard-container position-absolute right-0 top-0"> <clipboard-copy aria-label="Copy" class="ClipboardButton btn js-clipboard-copy m-2 p-0" data-copy-feedback="Copied!" data-tooltip-direction="w"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-copy js-clipboard-copy-icon m-2"> <path d="M0 6.75C0 5.784.784 5 1.75 5h1.5a.75.75 0 0 1 0 1.5h-1.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-1.5a.75.75 0 0 1 1.5 0v1.5A1.75 1.75 0 0 1 9.25 16h-7.5A1.75 1.75 0 0 1 0 14.25Z"></path><path d="M5 1.75C5 .784 5.784 0 6.75 0h7.5C15.216 0 16 .784 16 1.75v7.5A1.75 1.75 0 0 1 14.25 11h-7.5A1.75 1.75 0 0 1 5 9.25Zm1.75-.25a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Z"></path> </svg> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-check js-clipboard-check-icon color-fg-success d-none m-2"> <path d="M13.78 4.22a.75.75 0 0 1 0 1.06l-7.25 7.25a.75.75 0 0 1-1.06 0L2.22 9.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018L6 10.94l6.72-6.72a.75.75 0 0 1 1.06 0Z"></path> </svg> </clipboard-copy> </div> </template> <template id="snippet-clipboard-copy-button-unpositioned"> <div class="zeroclipboard-container"> <clipboard-copy aria-label="Copy" class="ClipboardButton btn btn-invisible js-clipboard-copy m-2 p-0 d-flex flex-justify-center flex-items-center" data-copy-feedback="Copied!" data-tooltip-direction="w"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-copy js-clipboard-copy-icon"> <path d="M0 6.75C0 5.784.784 5 1.75 5h1.5a.75.75 0 0 1 0 1.5h-1.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-1.5a.75.75 0 0 1 1.5 0v1.5A1.75 1.75 0 0 1 9.25 16h-7.5A1.75 1.75 0 0 1 0 14.25Z"></path><path d="M5 1.75C5 .784 5.784 0 6.75 0h7.5C15.216 0 16 .784 16 1.75v7.5A1.75 1.75 0 0 1 14.25 11h-7.5A1.75 1.75 0 0 1 5 9.25Zm1.75-.25a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Z"></path> </svg> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-check js-clipboard-check-icon color-fg-success d-none"> <path d="M13.78 4.22a.75.75 0 0 1 0 1.06l-7.25 7.25a.75.75 0 0 1-1.06 0L2.22 9.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018L6 10.94l6.72-6.72a.75.75 0 0 1 1.06 0Z"></path> </svg> </clipboard-copy> </div> </template> </div> <div id="js-global-screen-reader-notice" class="sr-only mt-n1" aria-live="polite" aria-atomic="true" ></div> <div id="js-global-screen-reader-notice-assertive" class="sr-only mt-n1" aria-live="assertive" aria-atomic="true"></div> </body> </html>