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===== Viral tagging reveals discrete populations in Synechococcus viral genome sequence space ===== | ===== Viral tagging reveals discrete populations in Synechococcus viral genome sequence space ===== | ||
+ | **Associate manuscript for all scripts on this page:** Deng, L., Ignacio-Espinoza, J.C., Gregory, A., Poulos, B.T., Weitz, J.S., Hugenholtz, P., Sullivan, M.B. (accepted). Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature. | ||
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+ | ==== recruitment ==== | ||
+ | {{:bioinformatics:scripts:recruitment.txt.zip}}\\ | ||
+ | **Author:** Julio Cesar Ignacio-Espinoza\\ | ||
+ | **Last Revision:** July 2011\\ | ||
==== Recruit2Cloud ==== | ==== Recruit2Cloud ==== | ||
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**Author:** Julio Cesar Ignacio-Espinoza\\ | **Author:** Julio Cesar Ignacio-Espinoza\\ | ||
**Last Revision:** Jan 2013\\ | **Last Revision:** Jan 2013\\ | ||
- | **Description:** plotSmall\\ | ||
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**Author:** Julio Cesar Ignacio-Espinoza\\ | **Author:** Julio Cesar Ignacio-Espinoza\\ | ||
**Last Revision:** Jan 2013\\ | **Last Revision:** Jan 2013\\ | ||
- | **Description:** SizeandLocation\\ | ||
==== rarefaction ==== | ==== rarefaction ==== | ||
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**Last Revision:** Nov 2013\\ | **Last Revision:** Nov 2013\\ | ||
**Description:** Generates a rarefaction curve from resampling a tabulated list of reads and its assigned protein cluster.\\ | **Description:** Generates a rarefaction curve from resampling a tabulated list of reads and its assigned protein cluster.\\ | ||
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==== dunns ==== | ==== dunns ==== | ||
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**Last Revision:** Nov 2013\\ | **Last Revision:** Nov 2013\\ | ||
**Description:** Generates a random distribution of values of Q. The effect size can be obtained by comparing this distribution to the observed values of Q.\\ | **Description:** Generates a random distribution of values of Q. The effect size can be obtained by comparing this distribution to the observed values of Q.\\ | ||
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+ | ==== matrix2PCA.m ==== | ||
+ | {{:bioinformatics:scripts:matrix2pca.m.zip}}\\ | ||
+ | **Author:** Julio Cesar Ignacio-Espinoza\\ | ||
+ | **Last Revision:** Dec 2013\\ | ||
+ | **Description:** Matlab list of commands, input is a m x n matrix where m is the number of observations and n is the number of variables measured.\\ | ||
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+ | ==== read2genome.pl ==== | ||
+ | {{:bioinformatics:scripts:read2genome.pl.zip}}\\ | ||
+ | **Author:** Julio Cesar Ignacio-Espinoza\\ | ||
+ | **Last Revision:** Dec 2013\\ | ||
+ | **Description:** The input files are a blastn file and a reference file. It aligns the best hits to the reference dataset, It outputs a per base frequency of nucleotides along the reference genome.\\ | ||
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+ | ==== randomGenome.pl ==== | ||
+ | {{:bioinformatics:scripts:randomgenome.pl.zip}}\\ | ||
+ | **Author:** Julio Cesar Ignacio-Espinoza\\ | ||
+ | **Last Revision:** Dec 2013\\ | ||
+ | **Description:** The input is the output of read2genome.pl. It generates a set of random contigs based on their per base frequency.\\ | ||
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+ | ==== chopGenome.pl ==== | ||
+ | {{:bioinformatics:scripts:chopgenome.pl.zip}}\\ | ||
+ | **Author:** Julio Cesar Ignacio-Espinoza\\ | ||
+ | **Last Revision:** Dec 2013\\ | ||
+ | **Description:** The input is a fasta file, it outputs a multi fasta file where the original file has been cut. | ||
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