Skip to content

Commit e4e4724

Browse files
bqminhbqminh
committed
update doc
1 parent a751d80 commit e4e4724

5 files changed

Lines changed: 38 additions & 28 deletions

File tree

‎doc/Compilation-Guide.md‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
11
---
22
layout: userdoc
33
title: "Compilation Guide"
4-
author: Dominik Schrempf, Jana Trifinopoulos, Minh Bui
5-
date: 2018-02-14
4+
author: Dominik Schrempf, Jana Trifinopoulos, Meaningseeking, Minh Bui
5+
date: 2020-07-22
66
docid: 20
77
icon: book
88
doctype: manual
@@ -113,7 +113,7 @@ Compiling under Mac OS X
113113
------------------------
114114
<div class="hline"></div>
115115

116-
>**TIP**: A ready made IQ-TREE package is provided by * [Homebrew](https://github.com/brewsci/homebrew-science/blob/master/Formula/iqtree.rb) by simply running `brew install homebrew/science/iqtree`.
116+
>**TIP**: A ready made IQ-TREE package is provided by * [Homebrew](https://github.com/brewsci/homebrew-science/blob/master/Formula/iqtree.rb) by simply running `brew install homebrew/science/iqtree2`.
117117
{: .tip}
118118

119119
* Make sure that Clang compiler is installed, which is typically the case if you installed Xcode and the associated command line tools.

‎doc/Frequently-Asked-Questions.md‎

Lines changed: 9 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
layout: userdoc
33
title: "Frequently Asked Questions"
44
author: Heiko Schmidt, Jana Trifinopoulos, M Bui, Minh Bui
5-
date: 2020-05-31
5+
date: 2020-10-28
66
docid: 9
77
icon: question-circle
88
doctype: manual
@@ -30,6 +30,8 @@ sections:
3030
url: how-do-i-save-time-for-standard-bootstrap
3131
- name: Why does IQ-TREE complain about the use of +ASC model?
3232
url: why-does-iq-tree-complain-about-the-use-of-asc-model
33+
- name: How does IQ-TREE treat identical sequences?
34+
url: how-does-iq-tree-treat-identical-sequences
3335
---
3436

3537
Frequently asked questions
@@ -239,6 +241,12 @@ All these sites must be removed from the alignment before a +ASC model can be ap
239241
>**TIP**: Starting with IQ-TREE version 1.5.0, an output alignment file with suffix `.varsites` is written in such cases, which contain only variable sites from the input alignment. The `.varsites` alignment can then be used with the +ASC model.
240242
{: .tip}
241243

244+
How does IQ-TREE treat identical sequences?
245+
-------------------------------------------
246+
247+
Among a group of identical sequences, IQ-TREE will keep the first two and ignore the rest. If the sequence is the 2nd one, it will be “kept for subsequent analysis”. If it is the 3rd or more, it will be “ignored but added at the end”. The rationale for this is to still be able to calculate the bootstrap support for this group of identical sequences: it is not always 100%. Because by bootstrap resampling, on average only two third of the sites will be present in a bootstrap alignment (due to sampling with replacement), and suddenly another sequence not in this group may actually become identical to this group of sequences. In that case, the bootstrap value will be < 100%.
248+
249+
Therefore, the `.uniqueseq.phy` printed by IQ-TREE may still contain the identical sequences, but no more than two of each identical group.
242250

243251
[Guindon et al., 2010]: https://doi.org/10.1093/sysbio/syq010
244252
[Minh et al., 2013]: https://doi.org/10.1093/molbev/mst024

‎doc/Quickstart.md‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
11
---
22
layout: userdoc
33
title: "Getting Started"
4-
author: Dominik Schrempf, M Bui, Minh Bui
5-
date: 2019-12-01
4+
author: Dominik Schrempf, M Bui, Meaningseeking, Minh Bui
5+
date: 2020-07-22
66
docid: 1
77
icon: info-circle
88
doctype: tutorial
@@ -50,7 +50,7 @@ Ready made IQ-TREE packages are available for the following distributions/reposi
5050
* [Debian Linux](https://packages.debian.org/unstable/science/iqtree): `sudo apt-get install iqtree`
5151
* [Arch Linux (AUR)](https://aur.archlinux.org/packages/iqtree-latest/)
5252
* [Anaconda](https://anaconda.org/bioconda/iqtree): `conda install -c bioconda iqtree`
53-
* [Homebrew](https://github.com/brewsci/homebrew-bio/blob/master/Formula/iqtree.rb): `brew install brewsci/bio/iqtree`
53+
* [Homebrew](https://github.com/brewsci/homebrew-bio/blob/master/Formula/iqtree.rb): `brew install brewsci/bio/iqtree2`
5454
* [FreeBSD](https://www.freshports.org/biology/iqtree/): `pkg install iqtree`
5555

5656
### Manual download

‎doc/iqtree-doc.pdf‎

1.4 KB
Binary file not shown.

‎index.html‎

Lines changed: 23 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -3,9 +3,11 @@
33
title: "IQ-TREE: Efficient phylogenomic software by maximum likelihood"
44
permalink: /
55
version: 1.6.12
6-
version_new: 2.0.6
6+
version_new: 2.1.2
77
releasedate: August 15, 2019
8-
releasedate_new: June 12, 2020
8+
releasedate_new: October 22, 2020
9+
v1_url: https://github.com/Cibiv/IQ-TREE/releases/download
10+
v2_url: https://github.com/iqtree/iqtree2/releases/download
911
---
1012
<!-- ========================== HEADER ========================== -->
1113
<div id="headerwrap">
@@ -16,15 +18,15 @@ <h1><img src="assets/img/iqtree-logo.svg" width="200"> IQ-TREE</h1>
1618
<h3>Efficient software for phylogenomic inference</h3>
1719
<h3>Stable release {{page.version}} ({{page.releasedate}})</h3>
1820
<p>
19-
<a id="downloadwin" style="display: none;" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version}}/iqtree-{{page.version}}-Windows.zip" class="btn btn-danger btn-lg" role="button">Download v{{page.version}} for Windows</a>
20-
<a id="downloadmac" style="display: none;" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version}}/iqtree-{{page.version}}-MacOSX.zip" class="btn btn-danger btn-lg" role="button">Download v{{page.version}} for macOS</a>
21-
<a id="downloadlinux" style="display: none;" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version}}/iqtree-{{page.version}}-Linux.tar.gz" class="btn btn-danger btn-lg" role="button">Download v{{page.version}} for Linux</a>
21+
<a id="downloadwin" style="display: none;" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-Windows.zip" class="btn btn-danger btn-lg" role="button">Download v{{page.version}} for Windows</a>
22+
<a id="downloadmac" style="display: none;" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-MacOSX.zip" class="btn btn-danger btn-lg" role="button">Download v{{page.version}} for macOS</a>
23+
<a id="downloadlinux" style="display: none;" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-Linux.tar.gz" class="btn btn-danger btn-lg" role="button">Download v{{page.version}} for Linux</a>
2224
</p>
23-
<h3>Release candidate {{page.version_new}} ({{page.releasedate_new}})</h3>
25+
<h3>COVID-19 release {{page.version_new}} ({{page.releasedate_new}})</h3>
2426
<p>
25-
<a id="downloadwin_new" style="display: none;" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version_new}}/iqtree-{{page.version_new}}-Windows.zip" class="btn btn-danger btn-lg" role="button">Download v{{page.version_new}} for Windows</a>
26-
<a id="downloadmac_new" style="display: none;" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version_new}}/iqtree-{{page.version_new}}-MacOSX.zip" class="btn btn-danger btn-lg" role="button">Download v{{page.version_new}} for macOS</a>
27-
<a id="downloadlinux_new" style="display: none;" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version_new}}/iqtree-{{page.version_new}}-Linux.tar.gz" class="btn btn-danger btn-lg" role="button">Download v{{page.version_new}} for Linux</a>
27+
<a id="downloadwin_new" style="display: none;" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-Windows.zip" class="btn btn-danger btn-lg" role="button">Download v{{page.version_new}} for Windows</a>
28+
<a id="downloadmac_new" style="display: none;" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-MacOSX.zip" class="btn btn-danger btn-lg" role="button">Download v{{page.version_new}} for macOS</a>
29+
<a id="downloadlinux_new" style="display: none;" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-Linux.tar.gz" class="btn btn-danger btn-lg" role="button">Download v{{page.version_new}} for Linux</a>
2830
</p>
2931
<p>
3032
<a id="downloadall" href="#download" class="btn btn-success btn-lg" role="button">All Downloads</a>
@@ -199,50 +201,50 @@ <h2>Download</h2>
199201
<i class="fa fa-windows"></i>
200202
<h4>Windows</h4>
201203
<div class="list-group">
202-
<a class="list-group-item list-group-item-info" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version}}/iqtree-{{page.version}}-Windows.zip">64-bit multicore Windows</a>
203-
<a class="list-group-item list-group-item-success" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version}}/iqtree-{{page.version}}-Windows32.zip">32-bit multicore Windows</a>
204+
<a class="list-group-item list-group-item-info" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-Windows.zip">64-bit multicore Windows</a>
205+
<a class="list-group-item list-group-item-success" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-Windows32.zip">32-bit multicore Windows</a>
204206
</div>
205207
</div>
206208

207209
<div class="col-sm-4">
208210
<i class="fa fa-apple"></i>
209211
<h4>macOS</h4>
210212
<div class="list-group">
211-
<a class="list-group-item list-group-item-info" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version}}/iqtree-{{page.version}}-MacOSX.zip">64-bit multicore macOS</a>
213+
<a class="list-group-item list-group-item-info" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-MacOSX.zip">64-bit multicore macOS</a>
212214
</div>
213215
</div>
214216

215217
<div class="col-sm-4">
216218
<i class="fa fa-linux"></i>
217219
<h4>Linux</h4>
218220
<div class="list-group">
219-
<a class="list-group-item list-group-item-info" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version}}/iqtree-{{page.version}}-Linux.tar.gz">64-bit multicore Linux</a>
220-
<a class="list-group-item list-group-item-success" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version}}/iqtree-{{page.version}}-Linux32.tar.gz">32-bit multicore Linux</a>
221-
<a class="list-group-item list-group-item-info" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version}}/iqtree-{{page.version}}-LinuxKNL.tar.gz">Xeon Phi Knights Landing Linux</a>
221+
<a class="list-group-item list-group-item-info" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-Linux.tar.gz">64-bit multicore Linux</a>
222+
<a class="list-group-item list-group-item-success" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-Linux32.tar.gz">32-bit multicore Linux</a>
223+
<!--<a class="list-group-item list-group-item-info" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-LinuxKNL.tar.gz">Xeon Phi Knights Landing Linux</a>-->
222224
</div>
223225
</div>
224226

225227
<div class="col-sm-12">
226-
<p>The release candidate {{page.version_new}} ({{page.releasedate_new}})</p>
228+
<p>COVID-19 release {{page.version_new}} ({{page.releasedate_new}})</p>
227229
</div>
228230

229231
<div class="col-sm-4">
230232
<div class="list-group">
231-
<a class="list-group-item list-group-item-info" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version_new}}/iqtree-{{page.version_new}}-Windows.zip">64-bit multicore Windows</a>
232-
<a class="list-group-item list-group-item-success" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version_new}}/iqtree-{{page.version_new}}-Windows32.zip">32-bit multicore Windows</a>
233+
<a class="list-group-item list-group-item-info" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-Windows.zip">64-bit multicore Windows</a>
234+
<!--<a class="list-group-item list-group-item-success" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-Windows32.zip">32-bit multicore Windows</a>-->
233235
</div>
234236
</div>
235237

236238
<div class="col-sm-4">
237239
<div class="list-group">
238-
<a class="list-group-item list-group-item-info" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version_new}}/iqtree-{{page.version_new}}-MacOSX.zip">64-bit multicore macOS</a>
240+
<a class="list-group-item list-group-item-info" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-MacOSX.zip">64-bit multicore macOS</a>
239241
</div>
240242
</div>
241243

242244
<div class="col-sm-4">
243245
<div class="list-group">
244-
<a class="list-group-item list-group-item-info" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version_new}}/iqtree-{{page.version_new}}-Linux.tar.gz">64-bit multicore Linux</a>
245-
<a class="list-group-item list-group-item-success" href="https://github.com/Cibiv/IQ-TREE/releases/download/v{{page.version_new}}/iqtree-{{page.version_new}}-Linux32.tar.gz">32-bit multicore Linux</a>
246+
<a class="list-group-item list-group-item-info" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-Linux.tar.gz">64-bit multicore Linux</a>
247+
<!--<a class="list-group-item list-group-item-success" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-Linux32.tar.gz">32-bit multicore Linux</a>-->
246248
</div>
247249
</div>
248250

0 commit comments

Comments
 (0)