adding quality control for alignments

rbturnbull / orthoflow

Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of protein-coding genes.

https://rbturnbull.github.io/orthoflow/

Apache License 2.0

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adding quality control for alignments #40

Closed JLSteenwyk closed 2 years ago

JLSteenwyk commented 2 years ago

It is worth considering adding a quality control steps. These could include

remove short trimmed alignments (less than 167 amino acid sites or 501 nucleotide sites)
remove sequences with low taxon occupancy (50% is a common threshold)
remove alignments where greater than 50% of the alignment was trimmed

rbturnbull commented 2 years ago

This is a great suggestion.

vinisalazar commented 2 years ago

I could try working on that tomorrow, do you have any suggested libraries that do this? Otherwise I will try using BioPython's Align module.

rbturnbull commented 2 years ago

Hi @vinisalazar - there are two tools we could use. I think Jacob's phykit (or a similar one of his packages) can do it. THere is also phytest which @smutch and I are working on in another project (https://phytest-devs.github.io/phytest/). We can talk about it tomorrow.