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matsengrp / historydag

https://matsengrp.github.io/historydag
GNU General Public License v3.0
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altered average_pairwise_rf_distance to avoid divide-by-zero in the c… #54

Closed marybarker closed 1 year ago

marybarker commented 1 year ago

…ase of a tree shaped DAG, and added option to apply Sankoff only to a subset of DAG nodes

marybarker commented 1 year ago

Great idea! Yeah, it would be good to do Sankoff on a subset of the sites, leaving the remainder fixed. This will take a bit of extra thought(I've made an issue #55), since sites are not independent and hence it will require either a method to compute transition cost for fully resolved sequences or else a the full-length cost vector expansion, even when only a subset of the sites are being recomputed.