[med-svn] [indelible] 04/11: Added documentation index page

Tue Dec 22 13:53:45 UTC 2015

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kloetzl-guest pushed a commit to branch master
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commit b2e13f502c9ceca5d4e433162ef658b5a870f981
Author: Fabian Klötzl <fabian at kloetzl.info>
Date:   Tue Dec 22 10:09:56 2015 +0100

    Added documentation index page
---
 .../0003-added-documentation-index-page.patch      | 35 ++++++++++++++++++++++
 debian/patches/series                              |  1 +
 2 files changed, 36 insertions(+)

diff --git a/debian/patches/0003-added-documentation-index-page.patch b/debian/patches/0003-added-documentation-index-page.patch
new file mode 100644
index 0000000..119acc3
--- /dev/null
+++ b/debian/patches/0003-added-documentation-index-page.patch
@@ -0,0 +1,35 @@
+From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian at kloetzl.info>
+Date: Tue, 22 Dec 2015 10:06:46 +0100
+Subject: added documentation index page
+
+---
+ help/index.html | 20 ++++++++++++++++++++
+ 1 file changed, 20 insertions(+)
+ create mode 100644 help/index.html
+
+diff --git a/help/index.html b/help/index.html
+new file mode 100644
+index 0000000..1ca680b
+--- /dev/null
++++ b/help/index.html
+@@ -0,0 +1,20 @@
++<!doctype html>
++<html>
++<head>
++	<title>Documentation for INDELible – A powerful and flexible simulator of biological evolution.</title>
++</head>
++<body>
++	<h1>INDELible</h1>
++	<p>INDELible is a new, portable, and flexible application for biological sequence simulation that combines many features in the same place for the first time. Using a length-dependent model of indel formation it can simulate evolution of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time.<br>
++
++	Nucleotide simulations may use the general unrestricted model or the general time reversible model and its derivatives, and amino-acid simulations can be conducted using fifteen different empirical rate matrices. Substitution rate heterogeneity can be modelled via the continuous and discrete gamma distributions, with or without a proportion of invariant sites. INDELible can also simulate under non-homogenous and non-stationary conditions where evolutionary models are permitted to chang [...]
++
++	Unique among indel simulation programs, INDELible offers the ability to simulate using codon models that exhibit nonsynonymous/synonymous rate ratio heterogeneity among sites and/or lineages.</p>
++	<hr>
++	<p>The model parameters are read from a file called <tt>control.txt</tt>. The following two sections explain the different parameters and their effect on the generated sequences.</p>
++	<ul>
++		<li><a href=examples.shtml>Tutorials and Examples</a></li>
++		<li><a href=manual.shtml>Manual</a></li>
++	</ul>
++</body>
++</html>
diff --git a/debian/patches/series b/debian/patches/series
index 028adcf..f13a164 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 0001-added-headers-for-getpid-2.patch
 0002-added-auto-tools-build-system.patch
+0003-added-documentation-index-page.patch

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