In the automatic word alignment the author MM automatically aligned the test sets from the partitions 2 8 in 6 batches.
COI sequences were manually aligned and 12S and 16S were automatically aligned using ClustalW multiple alignment implemented in BioEdit version 7.0.5.3 [22].
Sequences were automatically aligned using Sequencher 4.1 (Gene Code Corporation); the alignment was imported into MacClade 4.05 [52] and edited manually.
Recall, precision and F-score from the automatic word alignment when resources for the automatic word alignment were used cumulatively and all partitions were automatically aligned.
Recall, precision and F-score from the automatic word alignment when resources for the automatic word alignment were generated from all partitions and all partitions were automatically aligned.
Clustal W2 (http://www.ebi.ac.uk/Tools/msa/clustalw2/) was used to align protein sequences of 13 hRNaseA family members on the basis of automatically progressive alignment mode.
This additional domain-based analysis is capable of capturing important structural and evolutionary constraints (via priors) that are potentially missed when using an automatically collected alignment of homologous sequences.
However, Align-GVGD employs gene-specific alignments and its performance is severely affected when automatically generated alignments are used [Hicks et al., 2011].
Automatically derived alignments are prone to errors.
The automatically computed alignments were manually checked and minor corrections were introduced if so required.
