From: Parameterizing sequence alignment with an explicit evolutionary model
Alignment Accuracy | ||||||
---|---|---|---|---|---|---|
[ AUC for F measure (%)] | ||||||
Method | Global homology set | Local homology set | ||||
parameterization | parameterization | |||||
short | long | optimal | short | long | optimal | |
e2msa.afg | 71.4 | 80.4 | 80.3 | 68.2 | 68.2 | 73.6 |
e2msa.aga | 71.4 | 80.4 | 80.1 | 68.2 | 67.3 | 73.6 |
e2msa.aif | 71.3 | 80.4 | 80.2 | 68.1 | 68.3 | 73.3 |
e2msa.tkf92 | 71.2 | 80.0 | 79.9 | 68.1 | 68.2 | 73.4 |
e2msa.afr | 71.7 | 80.0 | 79.8 | 68.1 | 68.2 | 73.3 |
e2msa.aali | 71.0 | 78.7 | 78.6 | 67.9 | 66.4 | 72.7 |
e2msa.tkf91 | 69.5 | 75.4 | 74.5 | 66.2 | 69.1 | 70.7 |
PHMMER (no filters) SSEARCH | 78.7 | 72.9 | ||||
(BLOSUM62, -11/-1) | 80.0 | 71.7 | ||||
NCBIBLAST | 78.9 | 68.4 | ||||
MSAProbs | 81.7 | NA | ||||
MUSCLE | 80.8 | NA |