Calculate
Calculate - the group of commands for processing the calculations:
- Consensus - calculates a consensus.
- Conservation - calculates the conservatism of sequences. The conservatism is calculated in groups.
- Remove redundancy - removes the sequences with similarities to consensus below the threshold defined.
- Sort - Sequences' sorting modes:
- Sort by pairwise identity - sorts by pairwise identity.
- Sort by ID - sorts by alphabetical order. Sequences' IDs are used for sorting.
- Sort by group ID - sorts by groups first and then by alphabetical order inside a group.
- Principal Component Analysis - analysis of main components:
- Calculate - calculates main components.
- PCA 2D sequences - opens the "Sequence PCA Diagram 2D" window displaying two-dimensional
plot of sequences' principal components.
- PCA 3D sequences - opens the "Sequence PCA Diagram 3D" window displaying three-dimensional
plot of sequences' principal components.
- PCA 2D nucleotides - opens the "Nucleotide PCA Diagram 2D" window displaying two-dimensional
plot of nucleotides' principal components.
- PCA 3D nucleotides - opens the "Nucleotide PCA Diagram 3D" window displaying three-dimensional
plot of nucleotides' principal components.
Calculate all - to calculate the consensus, the conservatism and the principal components.
Auto calculate - to recalculate the consensus, the conservatism and the principal components after each removal of lines or columns.