Recent changes to Home

Home modified by John Archer

John Archer — Tue, 05 Jul 2022 12:29:15 -0000

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 **| linkedIn . web . orcid | **
-| [archer](https://www.linkedin.com/in/john-archer-7b872872/) . [web](https://cibio.up.pt/en/people/details/john-archer/) . [orcid](https://orcid.org/0000-0001-6212-0962) |---| [linheiro](https://www.linkedin.com/in/raquel-linheiro-50883873/) . web . [orcid](https://orcid.org/0000-0003-2659-0910) |---| [lobo](https://www.linkedin.com/in/diana-lobo-6aa63328/) . [web](https://cibio.up.pt/en/people/details/diana-lobo/) . [orcid](https://orcid.org/0000-0001-6988-9993) |---| sabatino . [web](https://cibio.up.pt/en/people/details/stephen-joseph-sabatino/) . [orcid](https://orcid.org/0000-0003-2815-2375) |
+| [linheiro](https://www.linkedin.com/in/raquel-linheiro-50883873/) . web . [orcid](https://orcid.org/0000-0003-2659-0910) |---| sabatino . [web](https://cibio.up.pt/en/people/details/stephen-joseph-sabatino/) . [orcid](https://orcid.org/0000-0003-2815-2375) |---| [lobo](https://www.linkedin.com/in/diana-lobo-6aa63328/) . [web](https://cibio.up.pt/en/people/details/diana-lobo/) . [orcid](https://orcid.org/0000-0001-6988-9993) |---| [archer](https://www.linkedin.com/in/john-archer-7b872872/) . [web](https://cibio.up.pt/en/people/details/john-archer/) . [orcid](https://orcid.org/0000-0001-6212-0962) |

Home modified by John Archer

John Archer — Tue, 05 Jul 2022 11:52:07 -0000

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 5. [TVScript](https://sourceforge.net/projects/tvscript/)


-**| linkedIn | web | orcid | **
+**| linkedIn . web . orcid | **
 | [archer](https://www.linkedin.com/in/john-archer-7b872872/) . [web](https://cibio.up.pt/en/people/details/john-archer/) . [orcid](https://orcid.org/0000-0001-6212-0962) |---| [linheiro](https://www.linkedin.com/in/raquel-linheiro-50883873/) . web . [orcid](https://orcid.org/0000-0003-2659-0910) |---| [lobo](https://www.linkedin.com/in/diana-lobo-6aa63328/) . [web](https://cibio.up.pt/en/people/details/diana-lobo/) . [orcid](https://orcid.org/0000-0001-6988-9993) |---| sabatino . [web](https://cibio.up.pt/en/people/details/stephen-joseph-sabatino/) . [orcid](https://orcid.org/0000-0003-2815-2375) |

Home modified by John Archer

John Archer — Tue, 05 Jul 2022 11:21:12 -0000

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 **Publication**
 Linheiro, R., Sabatino, S., Lobo, D., & Archer, J. (2022). CView: A network based tool for enhanced alignment visualization. PLOS ONE, 17(6), e0259726. [(view)]( https://doi.org/10.1371/JOURNAL.PONE.0259726)
+
+**Conference(s)**
+A poster that was (will be) presented at  [ISMB](https://www.iscb.org/ismb2022) is available [here](https://doi.org/10.5281/zenodo.6798044).

 **Getting Started**
 There are a number of ways to obtain help in relation to  CView:

Home modified by John Archer

John Archer — Wed, 15 Jun 2022 14:33:56 -0000

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 CView is an alignment visualizer that expands on the per-site representation of residues through the incorporation of a dynamic network that is based on the summarization of diversity present across different regions of the alignment. The relationship that sequence regions that are currently on screen have to other regions of diversity within the alignment can be observed, thus increasing intuitive insight.

 **Publication**
-Linheiro, R., Sabatino, S., LoboID, D., & ArcherID, J. (2022). CView: A network based tool for enhanced alignment visualization. PLOS ONE, 17(6), e0259726. [(view)]( https://doi.org/10.1371/JOURNAL.PONE.0259726)
+Linheiro, R., Sabatino, S., Lobo, D., & Archer, J. (2022). CView: A network based tool for enhanced alignment visualization. PLOS ONE, 17(6), e0259726. [(view)]( https://doi.org/10.1371/JOURNAL.PONE.0259726)

 **Getting Started**
 There are a number of ways to obtain help in relation to  CView:

Home modified by John Archer

John Archer — Wed, 15 Jun 2022 11:15:57 -0000

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+++ v41
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 CView is an alignment visualizer that expands on the per-site representation of residues through the incorporation of a dynamic network that is based on the summarization of diversity present across different regions of the alignment. The relationship that sequence regions that are currently on screen have to other regions of diversity within the alignment can be observed, thus increasing intuitive insight.

 **Publication**
-(publication under review)
-1. Linheiro R, Sabatino S, Lobo D, Archer J. *CView: A network based tool for enhanced alignment visualization.* bioRxiv. 2022; 2022.01.17.476623. [(view preprint)](https://doi.org/10.1101/2022.01.17.476623)
+Linheiro, R., Sabatino, S., LoboID, D., & ArcherID, J. (2022). CView: A network based tool for enhanced alignment visualization. PLOS ONE, 17(6), e0259726. [(view)]( https://doi.org/10.1371/JOURNAL.PONE.0259726)

 **Getting Started**
 There are a number of ways to obtain help in relation to  CView:

Home modified by John Archer

John Archer — Wed, 04 May 2022 15:33:01 -0000

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 3. The [Help] page explains the parameter options in detail.  
 4. Within the software there is help available in relation to both the interface and menu items  under the "Help" top menu. 

-Additionaly, the  alignmnet used within the manuscript case study is available from the Zenodo repository [here](https://doi.org/10.5281/zenodo.6475666) (doi no. 10.5281/zenodo.6475666). (This is different from the small test alignment that is downloades with the software and contained within the cview.zip file.)
+Additionaly, the  alignmnet used within the manuscript case study is available from the Zenodo repository [here](https://doi.org/10.5281/zenodo.6475666) (doi no. 10.5281/zenodo.6475666). 
+
+(This is different from the small test alignment that is contained within the cview.zip file.)

 **Abstract**
 To date basic visualization of sequence alignments have largely focused on displaying per-site columns of nucleotide, or amino acid, residues along with associated frequency summarizations. The persistence of this tendency to the more recent tools designed for the viewing of mapped read data indicates that such a perspective not only provides a reliable visualization of per-site alterations, but also offers implicit reassurance to the end user in relation to data accessibility. However, the initial insight gained is limited, something that is especially true when viewing alignments consisting of many sequences representing differing factors, such as geographical location, date and subtype. A basic alignment viewer can have potential to increase initial insight through visual enhancement, whilst not delving into the realms of complex sequence analysis. Here we present CView, a visualizer that expands on the per-site representation of residues through the incorporation of a dynamic network that is based on the summarization of diversity present across different regions of the alignment. Within the network nodes are based on the clustering of sequence fragments spanning windows that are placed consecutively along the alignment. Edges are placed between nodes of neighbouring windows where they share sequence id’s. Thus, if a single node is selected on the network, then the relationship that all sequences passing through that node have to other regions of diversity within the alignment can be instantly observed through the tracing of paths. In addition to augmenting visual insight, CView provides many export features including variant summarization, per-site residue and kmer frequency matrixes, consensus sequence generation, alignment dissection as well as general sequence clustering, each of which are useful across a range of research areas. The software has been designed to be user friendly, intuitive and interactive. It, along with source code, a quick start guide and test data, are available through the SourceForge project page: https://sourceforge.net/projects/cview/.

Home modified by John Archer

John Archer — Wed, 04 May 2022 15:32:11 -0000

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 **Getting Started**
 There are a number of ways to obtain help in relation to  CView:
-1. An **mp4  movie tutorial**, presented by  [Raquel Linheiro](https://orcid.org/0000-0003-2659-0910 ),  gives an overview of using CView and is available [here](https://zenodo.org/record/6514787). 
+1. An mp4  movie tutorial, presented by  [Raquel Linheiro](https://orcid.org/0000-0003-2659-0910 ),  gives an overview of using CView and is available [here](https://zenodo.org/record/6514787). **<<<<**
 2. The [QuickStart]  page explains how to download and run the software as well as obtain test data and source code. 
 3. The [Help] page explains the parameter options in detail.  
 4. Within the software there is help available in relation to both the interface and menu items  under the "Help" top menu.

Home modified by John Archer

John Archer — Wed, 04 May 2022 15:31:22 -0000

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 **Getting Started**
 There are a number of ways to obtain help in relation to  CView:
-1. An mp4  movie tutorial, presented by  [Raquel Linheiro](https://orcid.org/0000-0003-2659-0910 ),  gives an overview of using CView and is available [here](https://zenodo.org/record/6514787). 
+1. An **mp4  movie tutorial**, presented by  [Raquel Linheiro](https://orcid.org/0000-0003-2659-0910 ),  gives an overview of using CView and is available [here](https://zenodo.org/record/6514787). 
 2. The [QuickStart]  page explains how to download and run the software as well as obtain test data and source code. 
 3. The [Help] page explains the parameter options in detail.  
 4. Within the software there is help available in relation to both the interface and menu items  under the "Help" top menu. 
-5. A small additional PDF tutorial on variant identification is available at YYY.

 Additionaly, the  alignmnet used within the manuscript case study is available from the Zenodo repository [here](https://doi.org/10.5281/zenodo.6475666) (doi no. 10.5281/zenodo.6475666). (This is different from the small test alignment that is downloades with the software and contained within the cview.zip file.)

Home modified by John Archer

John Archer — Wed, 04 May 2022 12:34:33 -0000

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+++ v37
@@ -7,7 +7,7 @@

 **Getting Started**
 There are a number of ways to obtain help in relation to  CView:
-1. An mp4  movie tutorial, presented by  [Raquel Linheiro](https://orcid.org/0000-0003-2659-0910 ),  gives an overview of using CView and is available [here](https://zenodo.org/record/6514788). 
+1. An mp4  movie tutorial, presented by  [Raquel Linheiro](https://orcid.org/0000-0003-2659-0910 ),  gives an overview of using CView and is available [here](https://zenodo.org/record/6514787). 
 2. The [QuickStart]  page explains how to download and run the software as well as obtain test data and source code. 
 3. The [Help] page explains the parameter options in detail.  
 4. Within the software there is help available in relation to both the interface and menu items  under the "Help" top menu.

Home modified by John Archer

John Archer — Tue, 03 May 2022 17:01:42 -0000

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+++ v36
@@ -11,6 +11,7 @@
 2. The [QuickStart]  page explains how to download and run the software as well as obtain test data and source code. 
 3. The [Help] page explains the parameter options in detail.  
 4. Within the software there is help available in relation to both the interface and menu items  under the "Help" top menu. 
+5. A small additional PDF tutorial on variant identification is available at YYY.

 Additionaly, the  alignmnet used within the manuscript case study is available from the Zenodo repository [here](https://doi.org/10.5281/zenodo.6475666) (doi no. 10.5281/zenodo.6475666). (This is different from the small test alignment that is downloades with the software and contained within the cview.zip file.)