EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment.

ABSTRACT:

Background

Adding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with new data, adding sequences into a constraint alignment constructed using biological knowledge, or computing alignments in the presence of sequence length heterogeneity. Although this is a natural problem, only a few tools have been developed to use this information with high fidelity.

Results

We present EMMA (Extending Multiple alignments using MAFFT--add) for the problem of adding a set of unaligned sequences into a multiple sequence alignment (i.e., a constraint alignment). EMMA builds on MAFFT--add, which is also designed to add sequences into a given constraint alignment. EMMA improves on MAFFT--add methods by using a divide

SUBMITTER: Shen C 

PROVIDER: S-EPMC10704716 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature