Recent changes to Main

Main modified by Robert Kofler

Robert Kofler — Thu, 04 Feb 2016 09:42:47 -0000

Main modified by Robert Kofler

Robert Kofler — Thu, 04 Feb 2016 09:31:04 -0000

--- v9
+++ v10
@@ -32,6 +32,8 @@

 **[PoPoolation2](http://popoolation2.sourceforge.net/)**: Allows analyzing the population frequencies of SNPs from two or more populations. It may be used to identify differentiation between populations or to analyze data from genome wide association studies.

+**[PoPoolation TE2](https://sourceforge.net/projects/popoolation-te2/)** A tool for comparing the transposable element (TE) abundance between sample, where samples could be pooled populations, tissues or sequenced individuals. It identifies novel as well as known TE insertions and reports the population frequencies of all TEs in all samples.
+

 **[PoPoolation TE](http://popoolationte.sourceforge.net/)**: A quick and simple pipeline for the analysis of transposable element insertion frequencies in populations from pooled next generation sequencing data. PoPoolation TE identifies TE insertions that are present in the reference genome as well as novel TE insertions and estimates their population frequencies. This also allows for an comparision of TE insertion frequencies between different populations

Main modified by Robert Kofler

Robert Kofler — Thu, 25 Jun 2015 09:02:08 -0000

--- v8
+++ v9
@@ -10,9 +10,9 @@
 # Usage

   * [Quick walkthrough](TeachingPoPoolation)
-  * Detailed walkthrough: [PoPOOLationWalkthrough]
-  * Manual: [Manual]
-  * Slides from a course [Slides](http://drrobertkofler.wikispaces.com/PoPoolationGenomics)
+  * [Detailed walkthrough](PoPOOLationWalkthrough)
+  * [Manual](Manual)
+  * [Slides from a course](http://drrobertkofler.wikispaces.com/PoPoolationGenomics)

 # How to cite PoPoolation

Main modified by Robert Kofler

Robert Kofler — Thu, 25 Jun 2015 09:01:22 -0000

--- v7
+++ v8
@@ -9,7 +9,7 @@

 # Usage

-  * Quick walkthrough: [TeachingPoPoolation]
+  * [Quick walkthrough](TeachingPoPoolation)
   * Detailed walkthrough: [PoPOOLationWalkthrough]
   * Manual: [Manual]
   * Slides from a course [Slides](http://drrobertkofler.wikispaces.com/PoPoolationGenomics)

Main modified by Robert Kofler

Robert Kofler — Thu, 25 Jun 2015 08:58:40 -0000

--- v6
+++ v7
@@ -30,16 +30,15 @@

 **[Gowinda](http://gowinda.sourceforge.net/)**: unbiased analysis of gene set enrichement (e.g: Gene Ontology) for Genome Wide Association Studies. Gowinda may thus be used for biological interpretation of the results of PoPoolation and PoPoolation2:   

-**PoPoolation2**: Allows analyzing the population frequencies of SNPs from two or more populations. It may be used to identify differentiation between populations or to analyze data from genome wide association studies.
-http://popoolation2.sourceforge.net/
+**[PoPoolation2](http://popoolation2.sourceforge.net/)**: Allows analyzing the population frequencies of SNPs from two or more populations. It may be used to identify differentiation between populations or to analyze data from genome wide association studies.

-**PoPoolation TE**: A quick and simple pipeline for the analysis of transposable element insertion frequencies in populations from pooled next generation sequencing data. PoPoolation TE identifies TE insertions that are present in the reference genome as well as novel TE insertions and estimates their population frequencies. This also allows for an comparision of TE insertion frequencies between different populations http://popoolationte.sourceforge.net/

-**PoPoolation DB**: A user-friendly web-based database for the retrieval of natural variation in _Drosophila melanogaster_ 
-[PoPoolationDB](http://www.popoolation.at/pgt/)
+**[PoPoolation TE](http://popoolationte.sourceforge.net/)**: A quick and simple pipeline for the analysis of transposable element insertion frequencies in populations from pooled next generation sequencing data. PoPoolation TE identifies TE insertions that are present in the reference genome as well as novel TE insertions and estimates their population frequencies. This also allows for an comparision of TE insertion frequencies between different populations 
+
+**[PoPoolation DB](http://www.popoolation.at/pgt/)**: A user-friendly web-based database for the retrieval of natural variation in _Drosophila melanogaster_ 
+

 # Authors

   * [Robert Kofler](http://drrobertkofler.wikispaces.com/)
   * [Christian Schlötterer](http://i122server.vu-wien.ac.at/pop/lab_members/christian_schloetterer.html)
-

Main modified by Robert Kofler

Robert Kofler — Thu, 25 Jun 2015 08:57:40 -0000

--- v5
+++ v6
@@ -28,7 +28,7 @@

 # Partner projects

-**Gowinda**: unbiased analysis of gene set enrichement (e.g: Gene Ontology) for Genome Wide Association Studies. Gowinda may thus be used for biological interpretation of the results of PoPoolation and PoPoolation2:   http://gowinda.sourceforge.net/
+**[Gowinda](http://gowinda.sourceforge.net/)**: unbiased analysis of gene set enrichement (e.g: Gene Ontology) for Genome Wide Association Studies. Gowinda may thus be used for biological interpretation of the results of PoPoolation and PoPoolation2:   

 **PoPoolation2**: Allows analyzing the population frequencies of SNPs from two or more populations. It may be used to identify differentiation between populations or to analyze data from genome wide association studies.
 http://popoolation2.sourceforge.net/

Main modified by Robert Kofler

Robert Kofler — Thu, 25 Jun 2015 08:56:53 -0000

--- v4
+++ v5
@@ -28,18 +28,18 @@

 # Partner projects

-*Gowinda*: unbiased analysis of gene set enrichement (e.g: Gene Ontology) for Genome Wide Association Studies. Gowinda may thus be used for biological interpretation of the results of PoPoolation and PoPoolation2:   http://gowinda.sourceforge.net/
+**Gowinda**: unbiased analysis of gene set enrichement (e.g: Gene Ontology) for Genome Wide Association Studies. Gowinda may thus be used for biological interpretation of the results of PoPoolation and PoPoolation2:   http://gowinda.sourceforge.net/

-*PoPoolation2*: Allows analyzing the population frequencies of SNPs from two or more populations. It may be used to identify differentiation between populations or to analyze data from genome wide association studies.
+**PoPoolation2**: Allows analyzing the population frequencies of SNPs from two or more populations. It may be used to identify differentiation between populations or to analyze data from genome wide association studies.
 http://popoolation2.sourceforge.net/

-*PoPoolation TE*: A quick and simple pipeline for the analysis of transposable element insertion frequencies in populations from pooled next generation sequencing data. PoPoolation TE identifies TE insertions that are present in the reference genome as well as novel TE insertions and estimates their population frequencies. This also allows for an comparision of TE insertion frequencies between different populations http://popoolationte.sourceforge.net/
+**PoPoolation TE**: A quick and simple pipeline for the analysis of transposable element insertion frequencies in populations from pooled next generation sequencing data. PoPoolation TE identifies TE insertions that are present in the reference genome as well as novel TE insertions and estimates their population frequencies. This also allows for an comparision of TE insertion frequencies between different populations http://popoolationte.sourceforge.net/

-*PoPoolation DB*: A user-friendly web-based database for the retrieval of natural variation in _Drosophila melanogaster_ 
-[http://www.popoolation.at/pgt/]
+**PoPoolation DB**: A user-friendly web-based database for the retrieval of natural variation in _Drosophila melanogaster_ 
+[PoPoolationDB](http://www.popoolation.at/pgt/)

 # Authors

-  * Robert Kofler [http://drrobertkofler.wikispaces.com/]
-  * Christian Schlötterer [http://i122server.vu-wien.ac.at/pop/lab_members/christian_schloetterer.html]
+  * [Robert Kofler](http://drrobertkofler.wikispaces.com/)
+  * [Christian Schlötterer](http://i122server.vu-wien.ac.at/pop/lab_members/christian_schloetterer.html)

Main modified by Robert Kofler

Robert Kofler — Thu, 25 Jun 2015 08:55:29 -0000

--- v3
+++ v4
@@ -28,14 +28,14 @@

 # Partner projects

-*Gowinda*: unbiased analysis of gene set enrichement (e.g: Gene Ontology) for Genome Wide Association Studies. Gowinda may thus be used for biological interpretation of the results of !PoPoolation and !PoPoolation2:  http://code.google.com/p/gowinda/
+*Gowinda*: unbiased analysis of gene set enrichement (e.g: Gene Ontology) for Genome Wide Association Studies. Gowinda may thus be used for biological interpretation of the results of PoPoolation and PoPoolation2:   http://gowinda.sourceforge.net/

-*!PoPoolation2*: Allows analyzing the population frequencies of SNPs from two or more populations. It may be used to identify differentiation between populations or to analyze data from genome wide association studies.
-[http://code.google.com/p/popoolation2/]
+*PoPoolation2*: Allows analyzing the population frequencies of SNPs from two or more populations. It may be used to identify differentiation between populations or to analyze data from genome wide association studies.
+http://popoolation2.sourceforge.net/

-*!PoPoolation TE*: A quick and simple pipeline for the analysis of transposable element insertion frequencies in populations from pooled next generation sequencing data. !PoPoolation TE identifies TE insertions that are present in the reference genome as well as novel TE insertions and estimates their population frequencies. This also allows for an comparision of TE insertion frequencies between different populations [http://code.google.com/p/popoolationte].
+*PoPoolation TE*: A quick and simple pipeline for the analysis of transposable element insertion frequencies in populations from pooled next generation sequencing data. PoPoolation TE identifies TE insertions that are present in the reference genome as well as novel TE insertions and estimates their population frequencies. This also allows for an comparision of TE insertion frequencies between different populations http://popoolationte.sourceforge.net/

-*!PoPoolation DB*: A user-friendly web-based database for the retrieval of natural variation in _Drosophila melanogaster_ 
+*PoPoolation DB*: A user-friendly web-based database for the retrieval of natural variation in _Drosophila melanogaster_ 
 [http://www.popoolation.at/pgt/]

 # Authors

Main modified by Robert Kofler

Robert Kofler — Thu, 25 Jun 2015 08:52:41 -0000

--- v2
+++ v3
@@ -12,7 +12,7 @@
   * Quick walkthrough: [TeachingPoPoolation]
   * Detailed walkthrough: [PoPOOLationWalkthrough]
   * Manual: [Manual]
-  * Slides from a course [http://drrobertkofler.wikispaces.com/PoPoolationGenomics]
+  * Slides from a course [Slides](http://drrobertkofler.wikispaces.com/PoPoolationGenomics)

 # How to cite PoPoolation

Main modified by Robert Kofler

Robert Kofler — Thu, 25 Jun 2015 08:44:26 -0000

--- v1
+++ v2
@@ -1,21 +1,20 @@
-<wiki:toc max_depth="3"/>
+[TOC]

-= Introduction =
+# Introduction

 Currently next generation sequencing (NGS) technologies are mainly used to sequence individuals. However, the high coverage required and the resulting costs may be
 prohibitive for population scale studies. Sequencing pools of individuals instead may often be more cost effective and more accurate than sequencing individuals. PoPoolation is a pipeline for analysing pooled next generation sequencing data. PoPoolation builds upon open source tools (bwa, samtools) and uses standard file formats (gtf, sam, pileup) to ensure a wide compatibility. Currently PoPoolation allows to calculate Tajima’s Pi, Watterson’s Theta and Tajima’s D for reference sequences using a sliding window approach. Alternatively these population genetic estimators may be calculated for a set of genes (provided as gtf). One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. We believe that PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools.

-*Note a major novel version has been released: ReleaseNotes*

-= Usage =
+# Usage

-  * Quick walkthrough: TeachingPoPoolation
+  * Quick walkthrough: [TeachingPoPoolation]
   * Detailed walkthrough: [PoPOOLationWalkthrough]
   * Manual: [Manual]
   * Slides from a course [http://drrobertkofler.wikispaces.com/PoPoolationGenomics]

-= How to cite !PoPoolation =
+# How to cite PoPoolation

 Please cite the following two paper

@@ -27,7 +26,7 @@

-= Partner projects =
+# Partner projects

 *Gowinda*: unbiased analysis of gene set enrichement (e.g: Gene Ontology) for Genome Wide Association Studies. Gowinda may thus be used for biological interpretation of the results of !PoPoolation and !PoPoolation2:  http://code.google.com/p/gowinda/

@@ -39,9 +38,8 @@
 *!PoPoolation DB*: A user-friendly web-based database for the retrieval of natural variation in _Drosophila melanogaster_ 
 [http://www.popoolation.at/pgt/]

-= Authors =
+# Authors

   * Robert Kofler [http://drrobertkofler.wikispaces.com/]
   * Christian Schlötterer [http://i122server.vu-wien.ac.at/pop/lab_members/christian_schloetterer.html]

-