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The goal of this suite of scripts is to ease sequence retrieval of homologs and comparisons among them from multiple genomes. This wiki will show you some examples to use modules in homotools.

The geneseq page gives an example about how to extract gene sequences or gene annotation. The homocomp page shows how to run homologous searching and plot alignment comparison between two homologous sequences. You can run homocomp multiple times to extract homologs of interest from multiple genomes. These homologous sequences can be supplied to homograph for clustering and alignment visualization. The homograph page discusses its usage. Representative homologs can be aligned in a stack through the script homostack, whose example is shown in the homostack page. The homomine page explain how to run a pipeline to find homologous sequences and annotate all variants identified, including structural variation.