Remove invariant sites from large MSA
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2.4 years ago
lkatz • 0

I am looking for a Python or other script (or software package) to remove invariant sites from a large nucleotide multi-sequence alignment. Essentially, I am working towards creating a birds-eye view of variable sites among individuals. I'd appreciate any advice.

alignment sequence • 1.1k views
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2.0 years ago

You can try this "Script for removing or counting invariant sites for the RAxML ascertainment bias corrections"

https://github.com/btmartin721/raxml_ascbias

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2.0 years ago
Mensur Dlakic ★ 22k

BMGE is an entropy-based method that will automatically select the columns that are most informative. It does so in blocks, so individual conserved residues surrounded by variable columns may not be removed.

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