How do I strip alignment columns in R10 and above?

The “Strip Alignment Columns” function that was under the Tools menu in Geneious R9 and earlier has been replaced by a new “Mask Alignment” function in R10 and above.  

With this new tool you can either mask the sites by annotating the alignment, or create a copy of your alignment with the chosen sites removed.  


Alignments can be stripped or masked by codon position, identical sites or gap content as with the previous strip alignments function, or you can use a Nexus-style charset to specify particular regions of the alignment.    

Masked regions can be omitted from phylogenetic analyses by checking “Exclude masked sites” in the tree builder setup window.  

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