[adegenet-commits] r674 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Sep 23 11:52:37 CEST 2010
Author: jombart
Date: 2010-09-23 11:52:36 +0200 (Thu, 23 Sep 2010)
New Revision: 674
Modified:
www/acceuil.html
www/download.html
www/news.html
Log:
Updated pages
Modified: www/acceuil.html
===================================================================
--- www/acceuil.html 2010-09-23 09:33:46 UTC (rev 673)
+++ www/acceuil.html 2010-09-23 09:52:36 UTC (rev 674)
@@ -22,7 +22,8 @@
a
R
package
-for multivariate analysis, graphics, phylogeny and spatial
+for
+multivariate analysis, graphics, phylogeny and spatial
analysis. It is kindly hosted by <a
href="https://r-forge.r-project.org/projects/adegenet/" target="_top">R-Forge</a>.
<br>
@@ -59,6 +60,9 @@
STRUCTURE, Genepop, Fstat, Easypop, or any dataframe of genotypes<br>
- data import from <span style="font-weight: bold;">aligned DNA
sequences</span> to <span style="font-weight: bold;">SNPs</span><br>
+- data import from <span style="font-weight: bold;">aligned protein
+sequences</span> to polymorphic sites<span style="font-weight: bold;"></span>
+<img style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
- data <span style="font-weight: bold;">export</span> to the R
packages genetics, hierfstat, LDheatmap<br>
- handling of <span style="font-weight: bold;">different levels of
@@ -71,7 +75,8 @@
- basic <span style="font-weight: bold;">data information </span>(heterozygosity,
numbers
of
-alleles, sample sizes, ...)<br>
+alleles,
+sample sizes, ...)<br>
- <span style="font-weight: bold;">HWE</span> and <span
style="font-weight: bold;">G-statistic</span> <span
style="font-weight: bold;">tests</span>, F statistics implemented for
@@ -79,7 +84,9 @@
objects<br>
- computation of <span style="font-weight: bold;">genetic</span> <span
style="font-weight: bold;">distances<br>
-</span>- simulation of <span style="font-weight: bold;">hybridization<br>
+</span>- computation of <span style="font-weight: bold;">pairwise Fst </span><img
+ style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
+- simulation of <span style="font-weight: bold;">hybridization<br>
</span><span style="font-weight: bold;"></span>- methods for <span
style="font-weight: bold;">spatial
genetics: sPCA, </span><span style="font-weight: bold;">tests for
@@ -91,9 +98,10 @@
algorithm </span>for reconstructing genealogies of haplotypes<span
style="font-weight: bold;"><br>
</span>- simulation of <span style="font-weight: bold;">genealogies of
-haplotypes<br>
+haplotypes</span><img style="width: 80px; height: 37px;" alt=""
+ src="images/new.png"><br>
+<span style="font-weight: bold;"><br>
<br>
-<br>
</span><span style="text-decoration: underline;">Author:</span> Thibaut
Jombart
(<a target="_new" href="http://sites.google.com/site/thibautjombart/">website</a>)<br>
Modified: www/download.html
===================================================================
--- www/download.html 2010-09-23 09:33:46 UTC (rev 673)
+++ www/download.html 2010-09-23 09:52:36 UTC (rev 674)
@@ -18,15 +18,15 @@
<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
The
<span style="font-weight: bold;">current stable version</span>
-(adegenet_1.2-5)
+(adegenet_1.2-6)
is available as:<br>
-- <a href="files/adegenet_1.2-5.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-5.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-5.zip">Windows binary</a><br>
+- <a href="files/adegenet_1.2-6.tar.gz">linux/unix sources</a><br>
+- MacOS X binary<br>
+- <a href="files/adegenet_1.2-6.zip">Windows binary</a><br>
<br>
<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
The
-<span style="font-weight: bold;">devel version</span> (adegenet_1.2-6)
+<span style="font-weight: bold;">devel version</span> (adegenet_1.2-7)
is also available
from <a href="https://r-forge.r-project.org/scm/?group_id=120"
target="_top">R-Forge's
@@ -51,6 +51,11 @@
<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
<span style="font-weight: bold;">Older
versions</span>:<br>
+adegenet_1.2-5<br>
+- <a href="files/adegenet_1.2-5.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.2-5.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.2-5.zip">Windows binary</a><br>
+<br>
adegenet_1.2-4<br>
- <a href="files/adegenet_1.2-4.tar.gz">linux/unix sources</a><br>
- <a href="files/adegenet_1.2-4.tgz">MacOS X binary</a><br>
Modified: www/news.html
===================================================================
--- www/news.html 2010-09-23 09:33:46 UTC (rev 673)
+++ www/news.html 2010-09-23 09:52:36 UTC (rev 674)
@@ -18,7 +18,7 @@
style="font-weight: bold;"></span><br>
<span style="font-weight: bold;"></span>Current
stable version of <span style="color: rgb(255, 0, 0);">adegenet is
-1.2-5 </span>for R.2.11.1.<br>
+1.2-6 </span>for R.2.11.1.<br>
You can install the devel version from <a
href="https://r-forge.r-project.org/scm/?group_id=120">R-Forge</a>.<br>
See the current <a
@@ -28,14 +28,48 @@
Next major release will be 1.3-0, and will include the stable versions
of SeqTrack algorithm, DAPC, and new simulation tools.<br>
<br>
+<span style="font-weight: bold;">22/09/2010 <img
+ style="width: 80px; height: 37px;" alt="" src="images/new.png"></span><span
+ style="font-weight: bold;"></span><br>
+<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-6</span>)
+has
+been
+released
+for
+R-2.11.1!</big><span style="color: rgb(255, 0, 0);"><span
+ style="color: rgb(0, 0, 0);">
+This release adds the computation of pairwise Fst (</span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"><span
+ style="color: rgb(255, 0, 0);"></span><span
+ style="font-family: monospace; color: rgb(255, 0, 0);">?pairwise.fst</span></span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">) </span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">and
+a new function for extracting the polymorphism of aligned proteic
+sequences (class </span></span><span style="color: rgb(255, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"><span
+ style="font-family: monospace; color: rgb(255, 0, 0);">alignment </span></span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">in
+the seqinr package) into genind objects (</span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"><span
+ style="font-family: monospace; color: rgb(255, 0, 0);">?alignment2genind</span></span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">).
+See the </span></span><span style="color: rgb(255, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"></span></span><a
+ href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
+file for more information.</span></span><br>
+<br>
<span style="font-weight: bold;"><br>
-30/07/2010 <img style="width: 80px; height: 37px;" alt=""
- src="images/new.png"></span><span style="font-weight: bold;"></span><br>
+30/07/2010 </span><span style="font-weight: bold;"></span><br>
<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-5</span>)
has
been
released
-for R-2.11.1!</big><span style="color: rgb(255, 0, 0);"><span
+for
+R-2.11.1!</big><span style="color: rgb(255, 0, 0);"><span
style="color: rgb(0, 0, 0);">
This release includes a stable implementation of the <span
style="font-style: italic;">SeqTrack </span>algorithm </span></span><span
@@ -77,7 +111,8 @@
has
been
released
-for R-2.10.1 !</big><span style="color: rgb(255, 0, 0);"><span
+for
+R-2.10.1 !</big><span style="color: rgb(255, 0, 0);"><span
style="color: rgb(0, 0, 0);">
This release corrects a few issues and bugs from previous version, and
includes new material currently under review in scientific journals.
@@ -108,7 +143,8 @@
has
been
released
-for R.2.8.1 !</big><br>
+for
+R.2.8.1 !</big><br>
This is a important<span style="color: rgb(255, 0, 0);"><span
style="color: rgb(0, 0, 0);"> release, including some significant
improvements
@@ -127,7 +163,8 @@
time,
the
tutorial
-has been updated at the same time as the package
+has
+been updated at the same time as the package
release!<br>
<br>
<br>
@@ -137,12 +174,14 @@
has
been
released
-for R.2.8.0 !</big><br>
+for
+R.2.8.0 !</big><br>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This
new,
big
release
-implements many new things and corrects a few bugs
+implements
+many new things and corrects a few bugs
(see </span></span><a href="files/ChangeLog">ChangeLog</a><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
file). Amongst the biggest news, <span style="font-weight: bold;">several
@@ -155,12 +194,14 @@
which
can
represent
-genetic diversity using RGB scale, and a <span
+genetic
+diversity using RGB scale, and a <span
style="font-family: monospace; color: rgb(255, 0, 0);">loadingplot</span>,
which
can
be
-used to assess the most structuring alleles and loci in an
+used
+to assess the most structuring alleles and loci in an
analysis. A new georeferenced genetic dataset is also available
(dataset <span style="color: rgb(255, 0, 0); font-family: monospace;">rupica</span>).
And...
@@ -173,12 +214,14 @@
has
been
released
-for R.2.7.1 !</big><br>
+for
+R.2.7.1 !</big><br>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This
new
release
corrects
-a few bugs arising in version 1.2-0 (see </span></span><a
+a
+few bugs arising in version 1.2-0 (see </span></span><a
href="files/ChangeLog">ChangeLog</a><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
file), especially an issue with the detection of NAs. Documentation was
@@ -192,12 +235,14 @@
has
been
released
-for R.2.7.1 !</big><br>
+for
+R.2.7.1 !</big><br>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This
major
release
implements
-various levels of ploidy and adds some new
+various
+levels of ploidy and adds some new
features (see </span></span><a href="files/ChangeLog">ChangeLog</a><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
file):<br>
@@ -227,12 +272,14 @@
has
been
released
-for R.2.7.0 !</big><br>
+for
+R.2.7.0 !</big><br>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This
release
corrects
a
-few bugs and adds some new features (see </span></span><a
+few
+bugs and adds some new features (see </span></span><a
href="files/ChangeLog">ChangeLog</a><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
file):<br>
@@ -265,7 +312,8 @@
is
available
from
-the devel version of adegenet. It computes the <span
+the
+devel version of adegenet. It computes the <span
style="color: rgb(255, 0, 0);">proportion of shared alleles</span>
among a set of genotypes.<br>
<br>
@@ -276,12 +324,14 @@
has
been
released
-for R.2.6.2 !</big><br>
+for
+R.2.6.2 !</big><br>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This
release
corrects
a
-few bugs and adds some new features:<br>
+few
+bugs and adds some new features:<br>
- <span style="font-family: monospace;"></span></span></span><span
style="text-decoration: underline;">I/O:</span> <span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"><span
@@ -333,7 +383,8 @@
has
been
released
-for R.2.6.2.</small></big><br>
+for
+R.2.6.2.</small></big><br>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This
totally
new
@@ -389,7 +440,8 @@
and
adds
the
-following elements:<br>
+following
+elements:<br>
- <span style="font-family: monospace;"><span
style="color: rgb(255, 0, 0);">adegenetWeb</span> </span>is a simple
function opening the adegenet website in the default web browser.<br>
@@ -402,8 +454,8 @@
adding
a
genetic
-example, using <span
- style="font-family: monospace; color: rgb(255, 0, 0);">sim2pop</span><span
+example,
+using <span style="font-family: monospace; color: rgb(255, 0, 0);">sim2pop</span><span
style="color: rgb(255, 0, 0);"> </span>data.<br>
<span style="font-weight: bold;"><br>
<br>
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