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bioinformatics:scripts:popgen [2014/04/30 19:49]
chrissch
bioinformatics:scripts:popgen [2015/10/15 22:37] (current)
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 ===== Population Genomics ===== ===== Population Genomics =====
  
-==== Recruit2Cloud ==== 
-{{:​bioinformatics:​scripts:​recruit2cloud1-0-2.py.zip}}\\ 
-**Author:** Julio Cesar Ignacio-Espinoza\\ 
-**Last Revision:** Sep 2012\\ 
-**Description:​** Recruit2cloud01.pl takes a series of genome reads, a reference genome, and a blastn of the reference genome (in that order) to generate a COV file. Each line in the COV file corresponds to all the bases found in that position after aligning the reads to the blastn output with muscle. The first-order option and file descriptor and option represent the file with the return-delimited list of genome reads. The second-order option and file descriptor and option represents the file with the reference genome. The third-order option and file descriptor and option represents the file with the blastn output of the reference genome.\\ 
- 
-==== plotSmall ==== 
-{{:​bioinformatics:​scripts:​plotsmall.pl.zip}}\\ 
-**Author:** Julio Cesar Ignacio-Espinoza\\ 
-**Last Revision:** Jan 2013\\ 
-**Description:​** plotSmall\\ 
- 
- 
-==== SizeandLocation ==== 
-{{:​bioinformatics:​scripts:​sizeandlocation.pl.zip}}\\ 
-**Author:** Julio Cesar Ignacio-Espinoza\\ 
-**Last Revision:** Jan 2013\\ 
-**Description:​** SizeandLocation\\ 
  
 ==== DetectSynandNonSyn==== ==== DetectSynandNonSyn====
 {{:​bioinformatics:​scripts:​DetectSynandNonSyn.pl.zip}}\\ {{:​bioinformatics:​scripts:​DetectSynandNonSyn.pl.zip}}\\
 **Author:** Ann Gregory\\ **Author:** Ann Gregory\\
 +**Last Revision:** Apr 2014\\
 +**Description:​** From an alignment, this script will identify the total number of synonymous and nonsynonymous polymorphisms.
 +
  
 ==== MKselection ==== ==== MKselection ====
 {{:​bioinformatics:​scripts:​MKselection.pl.zip}}\\ {{:​bioinformatics:​scripts:​MKselection.pl.zip}}\\
 **Author:** Ann Gregory\\ **Author:** Ann Gregory\\
 +**Last Revision:** Apr 2014\\
 +**Description:​** Takes the input from detectsynandnonsyn.pl (above) and runs MK tests and determines if the gene is neutral, under positive selection or purifying selection.
 +
 +
  
 ==== remove_introns ==== ==== remove_introns ====
 {{:​bioinformatics:​scripts:​remove_introns.pl.zip}}\\ {{:​bioinformatics:​scripts:​remove_introns.pl.zip}}\\
 **Author:** Ann Gregory\\ **Author:** Ann Gregory\\
 +**Last Revision:** Apr 2014\\
 +**Description:​** Using a list of identified pairs of genes with potential introns, this script removes and concatenates the two gene ends into the singe gene.
 +
 +==== Syn_16S_Barcode_Identifier ====
 +{{:​bioinformatics:​scripts:​syn_16s_barcode_identifier.sh.zip}}\\
 +**Author:** Ann Gregory\\
 +**Last Revision:** June 2015\\
 +**Description:​**
  
 ==== unique_fixed_polymorphisms ==== ==== unique_fixed_polymorphisms ====
 {{:​bioinformatics:​scripts:​unique_fixed_polymorphisms.pl.zip}}\\ {{:​bioinformatics:​scripts:​unique_fixed_polymorphisms.pl.zip}}\\
 **Author:** Ann Gregory\\ **Author:** Ann Gregory\\
 +**Last Revision:** Apr 2014\\
 +**Description:​** Scans an alignment of population from two sites and looks for unique, fixed polymorphisms indicative of local adaptation.
  
  
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