This is a repository which comprises a bunch of information and scripts that I think can be useful for comparative genomics analyses:
Some of these scripts are part of different publications and are either in bitbucket repos or in the supplement of papers, I just wanted to centralize some of the most reusable resources by theme (e.g. microsynteny, orthology)
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Macrosynteny: make an oxford dotplot with R.
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Microsynteny: conserved blocks. Description of formats specific to the MicroSynteny tool (Simakov et al. 2013) can be found there.
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Orthology: deals with orthofinder >= 2.4 output to convert it into clus format.
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Other utils: small scripts for small tasks.
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Some Links: online tutorials/books that I found useful for teaching basics