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ParBLiSS / FastANI

Fast Whole-Genome Similarity (ANI) Estimation
Apache License 2.0
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can fastANI generate an alignment of conserved regions used for calculating ANI values? #77

Open limin321 opened 4 years ago

limin321 commented 4 years ago

Hi
I ran fastANI and used the output.txt to generate a distance matrix, after that, a neighbour joining tree was created using bionj_tree.R.
Feels like most people prefer ML tree built from conserved genes. I was wondering is it possible to have fastANI to generate an alignment of all conserved regions of all individuals used for comparison? In this way, I could just used this alignment to run a ML tree.

Also, since each genome will be used as both reference and query when calculating fastANI, does fastANI only take those single copy conserved region into account?

Sorry if my question is too easy for someone.

Thank you so much. Best LC

cjain7 commented 4 years ago

Hi, I'm not sure if this would help. If you give FastANI a single query genome and a single reference genome, along with --visualize parameter, it will spit out individual fragment mappings of conserved regions b/w the two genomes. This was originally done to enable visualisation.