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major update together with version 1.5.0
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bqminh committed Nov 1, 2016
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5 changes: 0 additions & 5 deletions README.md

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5 changes: 5 additions & 0 deletions _config.yml
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Expand Up @@ -119,3 +119,8 @@ about: IQ-TREE code is hosted at <a href="https://github.com/Cibiv/IQ-TREE">GitH
# author: Marcel Newman
# position: WEB DESIGNER - BLACKTIE.CO

#gems: [jekyll-paginate]
#paginate: 10
#paginate_path: "/blog/page:num/"
num_pages: 3

37 changes: 37 additions & 0 deletions _includes/displaynews.html
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@@ -0,0 +1,37 @@
{% assign numPages = 0 %}
{% assign latest_release = 0 %}
{% for post in site.posts %}
{% if post.categories contains "news" or post.categories contains "release" %}
<! -- Blog Post -->
{% if numPages >= page.entry_start %}
{% if numPages > page.entry_start %}
<br><div class="hline"></div>
{% endif %}
<h3>{{ post.title }}</h3>
<p>
<em>{{ post.date | date: "%b %-d, %Y" }}</em>
{% if post.categories contains "release" %}
<span class="label label-default">Release</span>
{% endif %}
{% for tag in post.tags %}
<span class="label label-default">{{ tag | capitalize }}</span>
{% endfor %}
</p>
{{ post.content }}
{% if post.categories contains "release" %}
{% if latest_release == 0 %}
<a href="{{site.baseurl}}/#download" class="btn btn-primary" role="button">Download latest version {{ post.version }}</a>
{% else %}
<a href="https://github.com/Cibiv/IQ-TREE/releases/tag/v{{ post.version }}" class="btn btn-primary" role="button">Download version {{ post.version }}</a>
{% endif %}
<br>
{% assign latest_release = latest_release | plus: 1 %}
{% endif %}
{% endif %}
{% assign numPages = numPages | plus: 1 %}
{% if numPages == page.entry_end %}
{% break %}
{% endif %}
{% endif %}
{% endfor %}

10 changes: 5 additions & 5 deletions _includes/nav.html
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Expand Up @@ -13,12 +13,12 @@
<div class="navbar-collapse collapse navbar-right">
<ul class="nav navbar-nav">
<li {% if page.title == "XXX" %}class="active"{% endif %}><a data-toggle="collapse" data-target=".navbar-collapse" href="{{"/#download" | prepend: site.baseurl }}">DOWNLOAD</a></li>
<li {% if page.title == "News" %}class="active"{% endif %}><a href="{{"/news/" | prepend: site.baseurl }}">NEWS</a></li>
<li {% if page.title == "News" %}class="active"{% endif %}><a href="{{"/news" | prepend: site.baseurl }}">NEWS</a></li>
<li {% if page.title == "XXX" %}class="active"{% endif %}><a href="http://iqtree.cibiv.univie.ac.at" target="_blank">WEB SERVICE</a></li>
<li {% if page.title == "Documentation" or page.categories.first == "doc" %}class="active"{% endif %}><a href="{{"/doc/" | prepend: site.baseurl }}">DOCUMENTATION</a></li>
<li {% if page.title == "FAQ" %}class="active"{% endif %}><a href="{{"/doc/Frequently-Asked-Questions/" | prepend: site.baseurl }}">FAQ</a></li>
<li {% if page.title == "About IQ-TREE" %}class="active"{% endif %}><a href="{{"/about/" | prepend: site.baseurl }}">ABOUT</a></li>
<li {% if page.title == "Documentation" or page.categories.first == "doc" %}class="active"{% endif %}><a href="{{"/doc" | prepend: site.baseurl }}">DOCUMENTATION</a></li>
<li {% if page.title == "FAQ" %}class="active"{% endif %}><a href="{{"/doc/Frequently-Asked-Questions" | prepend: site.baseurl }}">FAQ</a></li>
<li {% if page.title == "About IQ-TREE" %}class="active"{% endif %}><a href="{{"/about" | prepend: site.baseurl }}">ABOUT</a></li>
</ul>
</div><!--/.nav-collapse -->
</div>
</div>
</div>
16 changes: 16 additions & 0 deletions _includes/pagenav.html
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@@ -0,0 +1,16 @@
<nav aria-label="...">
<ul class="pager">
{% if page.pageid != 1 %}
{% if page.pageid == 2 %}
{% assign previd = '' %}
{% else %}
{% assign previd = page.pageid | minus: 1 %}
{% endif %}
<li><a href="../news{{previd}}"><span aria-hidden="true">&larr;</span> Newer posts</a></li>
{% endif %}
{% if page.pageid != site.num_pages %}
{% assign nextid = page.pageid | plus: 1 %}
<li><a href="../news{{nextid}}">Older posts <span aria-hidden="true">&rarr;</span></a></li>
{% endif %}
</ul>
</nav>
35 changes: 24 additions & 11 deletions _includes/sidebarnews.html
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@@ -1,13 +1,26 @@
<div class="well">
<h4>Recent news</h4>
<div class="row">
<div class="popular-posts">
{% for post in site.categories['news'] limit:10 %}
<div class="col-md-12 col-sm-6 col-xs-6">
<p><a href="{{ post.url | prepend: site.baseurl }}">{{ post.title }}</a><br><csmall>{{ post.date | date: "%b %-d, %Y" }}</csmall></p>
</div>
{% endfor %}
{% for alltag in site.tags %}
{% assign tag = alltag | first %}
{% if tag != 'tutorial' and tag != 'manual' %}
<div class="well">
<h4>Recent {{tag}}</h4>
<div class="row">
<div class="popular-posts">
{% assign numPages = 0 %}
{% for post in site.posts %}
{% if post.tags contains tag %}
<div class="col-md-12 col-sm-6 col-xs-6">
<p><a href="{{ post.url | prepend: site.baseurl }}">{{ post.title }}</a><br>
<csmall>{{ post.date | date: "%b %-d, %Y" }}</csmall>
</p>
</div>
{% assign numPages = numPages | plus: 1 %}
{% if numPages == 15 %}
{% break %}
{% endif %}
{% endif %}
{% endfor %}
</div>
</div>
</div>
<p><strong><a href="{{site.url}}/news">&#8594; See all news</a></strong></p>
</div>
{% endif %}
{% endfor %}
12 changes: 9 additions & 3 deletions _includes/sidebarrelease.html
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@@ -1,13 +1,19 @@
{% if num_releases %}
{% else %}
{% assign num_releases = 5 %}
{% endif %}
<div class="well">
<h4>Recent IQ-TREE releases</h4>
<h4>{% if num_releases == 5 %}Recent{% endif %} IQ-TREE releases</h4>
<div class="row">
<div class="popular-posts">
{% for post in site.categories['release'] limit:5 %}
{% for post in site.categories['release'] limit:num_releases %}
<div class="col-md-12 col-sm-6 col-xs-6">
<p><a href="{{ post.url | prepend: site.baseurl }}">Version {{ post.version }}</a><br><csmall>{{ post.date | date: "%b %-d, %Y" }}</csmall></p>
</div>
{% endfor %}
</div>
</div>
<p><strong><a href="{{site.url}}/release">&#8594; All release history</a></strong></p>
{% if num_releases == 5 %}
<p><strong><a href="{{site.baseurl}}/release">&#8594; All release history</a></strong></p>
{% endif %}
</div>
5 changes: 2 additions & 3 deletions _layouts/userdoc.html
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Expand Up @@ -9,8 +9,7 @@
<! -- SINGLE DOC -->
<div class="col-md-9">
<! -- User Doc -->
<h3>{{ page.title }}</h3>
<p><em>Last update: {{ page.date | date: "%b %-d, %Y" }} by {{ page.author }}</em></p>
<p><em>Last update: {{ page.date | date: "%b %-d, %Y" }}, Contributors: {{ page.author }}</em></p>

{{ content }}

Expand All @@ -31,4 +30,4 @@ <h3>{{ page.title }}</h3>
</div>

</div><! --/row -->
</div><! --/container -->
</div><! --/container -->
16 changes: 0 additions & 16 deletions _posts/blog/blog-template.md

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31 changes: 20 additions & 11 deletions _posts/doc/2015-11-07-Quickstart.md
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@@ -1,8 +1,8 @@
---
layout: userdoc
title: "Quickstart"
author: minh
date: 2015-12-01
author: Minh Bui
date: 2016-10-28
categories:
- doc
docid: 01
Expand All @@ -20,6 +20,10 @@ sections:
- name: Minimal command-line examples
url: minimal-command-line-examples
---

Getting started
===============

Recommended for users who just downloaded IQ-TREE the first time.
<!--more-->

Expand All @@ -31,6 +35,7 @@ Recommended for users who just downloaded IQ-TREE the first time.
- [For Windows users](#for-windows-users)
- [For Mac OS X users](#for-mac-os-x-users)
- [Minimal command-line examples](#minimal-command-line-examples)
- [Where to continue from here?](#where-to-continue-from-here)

<!-- END doctoc generated TOC please keep comment here to allow auto update -->

Expand All @@ -40,7 +45,7 @@ Installation

To achieve high performance IQ-TREE is a command-line program: you need to run IQ-TREE from a Terminal/Console (this is called Command Prompt under Windows). After you [downloaded IQ-TREE](../../#download), please:

* Extract the `.zip` (Windows, MacOSX) or `.tar.gz` (Linux) file to create a directory `iqtree-X.Y.Z-OS` or `iqtree-omp-X.Y.Z-OS`.
* Extract the `.zip` (Windows, MacOSX) or `.tar.gz` (Linux) file to create a directory `iqtree-X.Y.Z-OS` or `iqtree-omp-X.Y.Z-OS`, where `X.Y.Z` is the version number and `OS` is the operating system (Windows, MacOSX or Linux).
* You will find the executable in the `bin` sub-folder. Copy all files in `bin` folder to your system search path such that you can run IQ-TREE by entering `iqtree` or `iqtree-omp` from the Terminal.

Now you need to open a Terminal (or Console) to run IQ-TREE. See below the guide for [Windows users](#for-windows-users) and [Mac OS X users](#for-mac-os-x-users).
Expand All @@ -53,9 +58,9 @@ Since IQ-TREE is a command-line program, clicking on `iqtree.exe` will not work.

1. Click on "Start" menu (below left corner of Windows screen).
2. Type in "cmd" and press "Enter". It will open the Command Prompt window (see Figure below).
3. Go into IQ-TREE folder you just extracted by entering e.g.:
3. Go into IQ-TREE folder you just extracted by entering e.g. (assuming you downloaded version 1.5.0):

cd Downloads\iqtree-1.3.10-Windows
cd Downloads\iqtree-1.5.0-Windows
(assuming that IQ-TREE was downloaded into `Downloads` folder).
4. Now you can try an example run by entering:
Expand All @@ -65,7 +70,7 @@ Since IQ-TREE is a command-line program, clicking on `iqtree.exe` will not work.
(`example.phy` is the example PHYLIP alignment file also extracted in that folder).
5. After a few seconds, IQ-TREE finishes and you may see something like this:

![Windows command prompt](../../assets/img/doc/win-cmd2.png)
![Windows command prompt](../../assets/img/doc/win-cmd2.png)

Congratulations ;-) You have finished the first IQ-TREE analysis.

Expand All @@ -74,9 +79,9 @@ For Mac OS X users
------------------

1. Open the "Terminal", e.g., by clicking on the Spotlight icon (top-right corner), typing "terminal" and press "Enter".
2. Go into IQ-TREE folder by entering:
2. Go into IQ-TREE folder by entering (assuming you downloaded version 1.5.0):

cd Downloads/iqtree-1.2.0-MacOSX
cd Downloads/iqtree-1.5.0-MacOSX

(assuming that IQ-TREE was downloaded into `Downloads` folder).
3. Now you can try an example run by entering
Expand All @@ -86,7 +91,7 @@ For Mac OS X users
(`example.phy` is the example PHYLIP alignment file also extracted in that folder).
4. After a few seconds, IQ-TREE finishes and you may see something like this:

![Mac terminal](../../assets/img/doc/mac-cmd2.png)
![Mac terminal](../../assets/img/doc/mac-cmd2.png)

Congratulations ;-) You have finished the first IQ-TREE analysis.

Expand All @@ -97,8 +102,6 @@ Minimal command-line examples

A few typically analyses are listed in the following. Note that it is assumed that `iqtree` executable was already copied into system search path. If not, please replace `iqtree` with actual path to executable.

>**TIP**: Refer to [Beginner's tutorial](../Tutorial) for more details.
* Reconstruct maximum-likelihood tree from a sequence alignment (`example.phy`)
with the best-fit substitution model automatically selected:

Expand Down Expand Up @@ -132,3 +135,9 @@ A few typically analyses are listed in the following. Note that it is assumed th

iqtree -h

Where to continue from here?
----------------------------

Please continue with the **[Beginner's tutorial](../Tutorial)** for further usages.

8 changes: 6 additions & 2 deletions _posts/doc/2015-11-08-Advanced-Tutorial.md
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@@ -1,8 +1,8 @@
---
layout: userdoc
title: "Advanced Tutorial"
author: minh
date: 2016-06-21
author: Jana, Minh Bui
date: 2016-10-23
categories:
- doc
docid: 03
Expand All @@ -22,6 +22,10 @@ sections:
- name: Generating random trees
url: generating-random-trees
---

Advanced tutorial
=================

Recommended for experienced users to explore more features.
<!--more-->

Expand Down
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