<commit_before>---
layout: page
permalink: /software/pyrad/
title: "pyRAD"
modified: 2014-10-01 23:11
tags: [pyrad,software]
image:
  feature: header.png
  credit: <NAME>
  creditlink: 
share: 
---

---------------------   

#### Description

The benefit of _pyRAD_ over most alternative methods for analyzing RADseq-like data comes in its use of an alignment-clustering method (_vsearch_) that allows for the inclusion of indel variation which improves identification of homology across highly divergent samples. For this reason _pyRAD_ is commonly employed for RADseq studies at deeper phylogenetic scales, however, it works equally well at shallow scales.  

#### Flexibility

_pyRAD_ can analyze RAD, ddRAD, GBS, paired-end ddRAD and paired-end GBS data sets. It also has funtionality for trimming/removing adapter sequences and merging overlapping paired end reads. A two-step clustering method can be used to quickly cluster very large data sets with many hundreds of samples, or to direct the order of clustering with knowledge of phylogeny (useful for highly divergent sequences). A “split clustering” method can be used for paired-end ddRAD data allow greater divergence in second reads. As of v.3.0 clustering speeds in pyrad are dramatically improved.

#### Continued development
Below you can find the current release in addition to older releases. There is a “general use” tutorial which explains how to install and setup input files, and also tutorials with example data sets for different data types and analyses. The software was initially described in the following publication ([preprint](http://biorxiv.org/content/early/2013/12/03/001081), [journal](http://bioinformatics.oxfordjournals.org/content/early/2014/03/20/bioinformatics.btu121 ))  

### Downloads (now on github)  
+  [Current stable release](https://github.com/dereneaton/pyrad/releases)
+  [git Development version](https://github.com/dereneaton/pyrad/)

#### General Use Tutorial
+  [Full tutorial v.3.0](http://nbviewer.ipython.org/gist/dereneaton/af9548ea0e94bff99aa0/pyRAD_v.3.0.ipynb)  

#### I recommend going through an example tutorial which usually takes just a few minutes. 
+  [RADseq Tutorial v.3.0](http://nbviewer.ipython.org/gist/dereneaton/1f661bfb205b644086cc/tutorial_RAD.ipynb)  
+  [PE ddRAD Tutorial v.3.0](http://nbviewer.ipython.org/gist/dereneaton/1f661bfb205b644086cc/tutorial_RAD.ipynb)  
+  [PE ddRAD w/ merged reads Tutorial v.3.0](http://nbviewer.ipython.org/gist/dereneaton/1f661bfb205b644086cc/tutorial_RAD.ipynb)  
+  [SE GBS Tutorial v.3.0](http://nbviewer.ipython.org/gist/dereneaton/1f661bfb205b644086cc/tutorial_RAD.ipynb)  
+  [D-statistics tutorial]()  

--------------------------  

#### Google group questions forum ([link](https://groups.google.com/forum/#!forum/pyrad-users))

---------------------------  

#### Older version tutorials: 
+  [Full Tutorials](http://nbviewer.ipython.org/gist/dereneaton/af9548ea0e94bff99aa0)  
+  [RADseq Tutorial_2.16](http://nbviewer.ipython.org/gist/dereneaton/1f661bfb205b644086cc)
+  [RADseq Tutorial v.2.10](http://nbviewer.ipython.org/gist/dereneaton/1f661bfb205b644086cc/pyRAD_v.2.10.ipynb)    
+  [PE ddRAD Tutorial_2.16](http://nbviewer.ipython.org/gist/dereneaton/1f661bfb205b644086cc/tutorial_RAD.ipynb)  


#### Older version downloads (pre-git versions)
[Tutorial\_pyRAD\_v.2.01+ (old)](/tutorial/pyrad_v.2.1/)  
[pyrad_v.2.15.zip](/downloads/pyrad_v.2.15.zip)  
[pyrad_v.2.14.zip](/downloads/pyrad_v.2.14.zip)  
[pyrad_v.2.13.zip](/downloads/pyrad_v.2.13.zip)  
[pyrad_v.2.12.zip](/downloads/pyrad_v.2.12.zip)   
[pyrad_v.2.11.zip](/downloads/pyrad_v.2.11.zip)  
[pyrad_v.2.10.zip](/downloads/pyrad_v.2.10.zip)   
[pyrad_v.2.01 tutorial](http://nbviewer.ipython.org/gist/dereneaton/af9548ea0e94bff99aa0)  
[pyrad_v.2.01.zip](/downloads/pyrad_v.2.01.zip)  
[pyrad_v.2.00.zip](/downloads/pyrad_v.2.0.zip)  
[pyrad_v.1.64.zip](/downloads/pyrad_v.1.64.zip)  
[pyrad\_tutorial\_v.1.64.pdf](/downloads/pyrad_v.1.64.pdf)  
[pyrad_v.1.4.zip](/downloads/pyrad_v.1.4.zip)  <commit_msg>3.0 full tutorial up<commit_after>---
layout: page
permalink: /software/pyrad/
title: "pyRAD"
modified: 2014-10-01 23:11
tags: [pyrad,software]
image:
  feature: header.png
  credit: <NAME>
  creditlink: 
share: 
---

---------------------   

#### Description

The benefit of _pyRAD_ over most alternative methods for analyzing RADseq-like data comes in its use of an alignment-clustering method (_vsearch_) that allows for the inclusion of indel variation which improves identification of homology across highly divergent samples. For this reason _pyRAD_ is commonly employed for RADseq studies at deeper phylogenetic scales, however, it works equally well at shallow scales.  

#### Flexibility

_pyRAD_ can analyze RAD, ddRAD, GBS, paired-end ddRAD and paired-end GBS data sets. Below you can find the current release in addition to older releases. There is a “general use” tutorial which explains how to install and setup input files, and also tutorials with example data sets for different data types and analyses. The software was initially described in the following publication ([preprint](http://biorxiv.org/content/early/2013/12/03/001081), [journal](http://bioinformatics.oxfordjournals.org/content/early/2014/03/20/bioinformatics.btu121 ))  

### Downloads (now on github)  
+  [Current stable release](https://github.com/dereneaton/pyrad/releases)
+  [git Development version](https://github.com/dereneaton/pyrad/)

#### General Use Tutorial
+  [Full tutorial v.3.0](http://nbviewer.ipython.org/gist/dereneaton/af9548ea0e94bff99aa0/pyRAD_v.3.0.ipynb)  

#### Recommended example Tutorial  
+  [SE RAD Tutorial v.3.0](http://nbviewer.ipython.org/gist/dereneaton/1f661bfb205b644086cc/tutorial_RAD_3.0.ipynb)  

#### Advanced tutorials  
+  [PE ddRAD Tutorial v.3.0](http://nbviewer.ipython.org/gist/dereneaton/dc6241083c912519064e/tutorial_pairddRAD_3.0.ipynb)  
+  [PE ddRAD w/ merged reads Tutorial v.3.0](http://nbviewer.ipython.org/gist/dereneaton/dc6241083c912519064e/tutorial_pairddRAD_3.0-merged.ipynb)  
+  SE GBS Tutorial v.3.0()
+  PE GBS Tutorial v.3.0()
+  D-statistics tutorial()  

--------------------------  

#### Google group questions forum ([link](https://groups.google.com/forum/#!forum/pyrad-users))

---------------------------  

#### Older version tutorials: 
+  [Full Tutorials](http://nbviewer.ipython.org/gist/dereneaton/af9548ea0e94bff99aa0)  
+  [RADseq Tutorial_2.16](http://nbviewer.ipython.org/gist/dereneaton/1f661bfb205b644086cc)
+  [RADseq Tutorial v.2.10](http://nbviewer.ipython.org/gist/dereneaton/1f661bfb205b644086cc/pyRAD_v.2.10.ipynb)    
+  [PE ddRAD Tutorial_2.16](http://nbviewer.ipython.org/gist/dereneaton/1f661bfb205b644086cc/tutorial_RAD.ipynb)  


#### Older version downloads (pre-git versions)
[Tutorial\_pyRAD\_v.2.01+ (old)](/tutorial/pyrad_v.2.1/)  
[pyrad_v.2.15.zip](/downloads/pyrad_v.2.15.zip)  
[pyrad_v.2.14.zip](/downloads/pyrad_v.2.14.zip)  
[pyrad_v.2.13.zip](/downloads/pyrad_v.2.13.zip)  
[pyrad_v.2.12.zip](/downloads/pyrad_v.2.12.zip)   
[pyrad_v.2.11.zip](/downloads/pyrad_v.2.11.zip)  
[pyrad_v.2.10.zip](/downloads/pyrad_v.2.10.zip)   
[pyrad_v.2.01 tutorial](http://nbviewer.ipython.org/gist/dereneaton/af9548ea0e94bff99aa0)  
[pyrad_v.2.01.zip](/downloads/pyrad_v.2.01.zip)  
[pyrad_v.2.00.zip](/downloads/pyrad_v.2.0.zip)  
[pyrad_v.1.64.zip](/downloads/pyrad_v.1.64.zip)  
[pyrad\_tutorial\_v.1.64.pdf](/downloads/pyrad_v.1.64.pdf)  
[pyrad_v.1.4.zip](/downloads/pyrad_v.1.4.zip)  
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