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xingjianleng / DBGA

The repository for the genome sequence alignment research project
BSD 3-Clause "New" or "Revised" License
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where is the guide tree estimated? #21

Open GavinHuttley opened 1 year ago

GavinHuttley commented 1 year ago

Lines of code where dbga is estimating the guide-tree.

xingjianleng commented 1 year ago

In the latest implementation, the DistanceMatrix object from cogent3 was used in de Bruijn MSA. The DistanceMatrix was one input parameter for the alignment() function. The guide tree was constructed at the beginning of alignment.

The current implementation for estimating the DistanceMatrix doesn't have any mathematical/biological meaning, especially how k_estimated is calculated. The implementation is at https://github.com/xingjianleng/DBGA/blob/0da8dca853a98168dd858ad826b126827ee322b9/src/dbga/utils.py#L416-L437