for-giobbe/BASE
Pronunced /'baze/ - is a tool which allows to integrate non-ubiquitous genes in comparative genomics analyses for selection.
BASE - pronunced /'baze/ - is a workflow built to ease the inference and interpretation of selection regimes in the context of comparative genomics.
While the majority of these analyses are restricted to ubiquitous genes - i.e. genes which are present in all the species considered -
BASE allows to integrate non-ubiquitous genes - i.e. genes which are not present in all the species considered - in a straightforward and reproducible manner.
Nonetheless, BASE presents many other features, including replicates, gene-trees and species-trees analyses.
BASE has been designed to function in two indipendent steps:
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analyze infer & compare a general and alternative models for each gene.
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extract retrive metrics of branches and/or clades, allowing a treshold for missing species.
More information on each mode can be accessed by typing --analize or --extract followed by -h.
BASE leverages several other pieces of software, most notably codeml. Here is the workflow schematic:
You can find informations on installation and usage following the relative tutorials.
A preprint for BASE is available here.
For troubleshooting or any explanation on BASE functioning and usage write to forni.giobbe@gmail.com.