Merge branch 'master' of https://github.com/SegataLab/panphlan

Author: leonarDubois

README.md

@@ -10,12 +10,12 @@ microbial population studies.
 
 PanPhlAn is written in Python and covers the three main tasks:
 
-* `panphlan_pangenome_generation.py`, to create the pangenome database of a bacterial species
-  [→ read more](https://bitbucket.org/CibioCM/panphlan/wiki/panphlan_pangenome_generation)
-* `panphlan_map.py`, to profile each metagenomic sample by mapping it against the species specific database
-  [→ read more](https://bitbucket.org/CibioCM/panphlan/wiki/panphlan_map)
-* `panphlan_profile.py`, to merge and process the mapping results for getting the final gene presence/absence and transcriptional matrices
-  [→ read more](https://bitbucket.org/CibioCM/panphlan/wiki/panphlan_profile)
+* `panphlan_pangenome_generation.py`, to create the pangenome database of a bacterial species  
+  [read more](https://github.com/SegataLab/panphlan/wiki/Pangenome-generation)
+* `panphlan_map.py`, to profile each metagenomic sample by mapping it against the species specific database  
+  [read more](https://github.com/SegataLab/panphlan/wiki/PanPhlAn-mapping)
+* `panphlan_profile.py`, to merge and process the mapping results for getting the final gene presence/absence and transcriptional matrices  
+  [read more](https://github.com/SegataLab/panphlan/wiki/PanPhlAn-profiling)
 
 
 
@@ -25,14 +25,14 @@ PanPhlAn runs under Ubuntu/Linux and requires the following software tools to be
 * Samtools
 * Python 3.x (including the Biopython module)
 
-For more information, see our wiki [→ Download and Installation](https://bitbucket.org/CibioCM/panphlan/wiki/Download_and_Installation).
+For more information, see our wiki [Download and Installation](https://github.com/SegataLab/panphlan/wiki#download-the-panphlan-software).
 
 ## Contact & User support ##
 
-[→ User Tutorial](https://bitbucket.org/CibioCM/panphlan/wiki)
+A [user tutorial](https://github.com/SegataLab/panphlan/wiki/Tutorial) is available on the [PanPhlAn wiki](https://github.com/SegataLab/panphlan/wiki). For help, use also the [bioBakery help forum](https://forum.biobakery.org/).
+
 
 The PanPhlAn software team: [Matthias Scholz](http://www.matthias-scholz.de/) (algorithm design), [Thomas Tolio](https://www.linkedin.com/in/thomastolio) (programmer), Leonard Dubois and [Nicola Segata](http://segatalab.cibio.unitn.it/) (principal investigator).  
-For help, use the [bioBakery help forum](https://forum.biobakery.org/).
 
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