<commit_before># Documentation for script: _mkProteinClusters.pl_

## Summary
This program performs hierarchical clustering of a set of proteins based on 
their BLAST scores and reports a dendogram. The scores can also be estimated 
using other programs, such as UBLAST, or the Smith-Waterman algorithm as 
implemented in SSEARCH. Several methods for merging clusters are 
supported (e.g., Ward, single-linkage, average linkage, etc.). The clustering 
is performed using the R statistical computing environment.


## Contributor
<NAME>  


## How to cite this program
If you find this program useful, please cite the paper:  

  * <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>. 
  _Bioinformatic characterization of the Anoctamin Superfamily of Ca2+-activated ion 
  channels and lipid scramblases._  2018. PLoS One. **13**(3):e0192851 
  **PMID:** [29579047](https://www.ncbi.nlm.nih.gov/pubmed/?term=29579047)  


## Dependencies
The following programs need to be available in your path for this 
program to run properly:

1. **_blast+ 2.6.0 to 2.10.0_**  
Other versions of blast may require minor adaptations. Visit the
[download site](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download). 

2. **_ssearch36 version: 36.3.8e_**  
Other versions of ssearch may require minor adaptations. Visit the
[download site](https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml). 
<commit_msg>Update mkProteinClusters.md<commit_after># Documentation for script: _mkProteinClusters.pl_

## Summary
This program performs hierarchical clustering of a set of proteins based on 
their [_BLAST_](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) 
scores and reports a dendogram. The scores can also be estimated using other programs, such as 
[_UBLAST_](https://www.drive5.com/usearch/manual/ublast_algo.html), or the Smith-Waterman algorithm as 
implemented in [_SSEARCH_](https://fasta.bioch.virginia.edu/fasta_www2/fasta_class.shtml). 
Several methods for merging clusters are supported (e.g., Ward, single-linkage, average linkage, etc.). The clustering 
is performed using the [_R_](https://www.r-project.org/) statistical computing environment.


## Contributor
<NAME>  


## How to cite this program
If you find this program useful, please cite the paper:  

  * <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>. 
  _Bioinformatic characterization of the Anoctamin Superfamily of Ca2+-activated ion 
  channels and lipid scramblases._  2018. PLoS One. **13**(3):e0192851 
  **PMID:** [29579047](https://www.ncbi.nlm.nih.gov/pubmed/?term=29579047)  


## Dependencies
The following programs need to be available in your path for this 
program to run properly:

1. **_blast+ 2.6.0 to 2.10.0_**  
Other versions of blast may require minor adaptations. Visit the
[download site](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download). 

2. **_ssearch36 version: 36.3.8e_**  
Other versions of ssearch may require minor adaptations. Visit the
[download site](https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml). 

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