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bioinformatics:scripts:popgen [2014/05/01 14:49] 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\\ | ||
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- | ==== SizeandLocation ==== | ||
- | {{:bioinformatics:scripts:sizeandlocation.pl.zip}}\\ | ||
- | **Author:** Julio Cesar Ignacio-Espinoza\\ | ||
- | **Last Revision:** Jan 2013\\ | ||
- | **Description:** SizeandLocation\\ | ||
==== DetectSynandNonSyn==== | ==== DetectSynandNonSyn==== | ||
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**Last Revision:** Apr 2014\\ | **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. | **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 ==== |