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geronimp / graftM

GraftM - Rapid community profiles from metagenomes
http://geronimp.github.io/graftM/
GNU General Public License v3.0
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mafft-linsi or similar as default for create alignment #218

Closed geronimp closed 7 years ago

geronimp commented 8 years ago

Accurate phylogenetic placement relies on good alignment of both the reference sequences used to build the tree, and the query sequences to be inserted. We can help on the reference tree side of things by making the default alignment algorithm more robust (by using mafft-linsi). Obviously for larger alignments this wont be feasible. But its something to look into to improve reference alignments when we have, say, <500 sequences?

Joel

wwood commented 8 years ago

mafft by itself chooses the best algorithm based on the number of input sequences, IIRC. Are the default choices not aligning with what we want?