SynMap: Difference between revisions
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[[Image:Master 3068 8.CDS-CDS.blastn geneorder D20 g10 A5.w2000.ks.hist-1.png|thumb|right|600px|Histogram of synonymous rate change data for syntenic gene pairs between Arabidopsis thaliana and Arabidopsis lyrata.]] | [[Image:Master 3068 8.CDS-CDS.blastn geneorder D20 g10 A5.w2000.ks.hist-1.png|thumb|right|600px|Histogram of synonymous rate change data for syntenic gene pairs between Arabidopsis thaliana and Arabidopsis lyrata.]] | ||
[[Image:SynPlot-Chr1-At-v-Al.png|thumb|right|600px|Syntenic dotplot and synonymous substitution histogram of Chromosome 1 of Arabidopsis thaliana and Arabidopsis lyrata. Syntenic gene pairs were identified by DAGChainer, and colored based on their synonymous substitution rate as calculated by CodeML. Syntenic regions derived from speciation (orthologs) or from the shared whole genome duplication events (alpha and beta) are labeled. These images were generated by SynMap and can be viewed at generated by SynMap at http://toxic.berkeley.edu/CoGe//diags/Arabidopsis_lyrata/Arabidopsis_thaliana_thale_cress/html/3068_8.CDS-CDS.blastn.dag_geneorder_D20_g10_A5.scaffold_1-1.w600.ks.html]] | |||
Revision as of 16:47, 28 August 2009
Overview
Specifying genomes
DAGChainer options
SynMap options
Calculating and displaying synonymous/non-synonymous (kS, kN) data
Interacting with results
Example Results
