Alignment Menu (in Alignment Explorer)

This menu provides access to commands for editing the sequence data in the alignment grid.  The commands are:

Align by ClustalW: This option is used to align the DNA or protein sequence included in the current selection on the alignment grid. You will be prompted for the alignment parameters (which are context sensitive for DNAHC_CLUSTALW_Options_DNA_Dialog or ProteinHC_CLUSTALW_Options_Protein_Dialog sequence data) to be used in ClustalW ClustalW is a general purpose multiple sequence alignment program for DNA or proteins. You can learn more about ClustalW by visiting its website (http://www.ebi.ac.uk/clustalw/).; to accept the parameters, press “OK”. This initiates the ClustalW ClustalW is a general purpose multiple sequence alignment program for DNA or proteins. You can learn more about ClustalW by visiting its website (http://www.ebi.ac.uk/clustalw/). alignment system. Alignment Builder then aligns the current selection in the alignment grid using the accepted parameters.

Align by ClustalW (Codons): This option is used to align (via ClustalW ClustalW is a general purpose multiple sequence alignment program for DNA or proteins. You can learn more about ClustalW by visiting its website (http://www.ebi.ac.uk/clustalw/).) the coding sequence data in the current selection by first translating all codons to amino acids, performing the alignment, and finally replacing the amino acids with the original codons.

Align by MUSCLE: This option is used to align the DNA or protein sequence included in the current selection on the alignment grid.  You will be prompted for the alignment parameters (DNAMUSCLE_Options_DNA_ or ProteinMUSCLE_Options_Protein_) to be used in MUSCLE; to accept the parameters, press “OK”. This initiates the MUSCLE alignment system. Alignment Builder then aligns the current selection in the alignment grid using the accepted parameters.

Align by MUSCLE (Codons): This option is used to align (via MUSCLE) the coding sequence data in the current selection by first translating all codons to amino acids, performing the alignment, and finally replacing the amino acids with the original codons.

Mark/Unmark Site: This marks or unmarks a single site in the alignment grid. Each sequence in the alignment may only have one site marked at a time. Modifications can be made to the alignment by marking two or more sites and then aligning them using the Align Marked Sites function.

Align Marked Sites: This aligns marked sites. Two or more sites in the alignment must be marked for this function to have an effect.

Unmark All Sites: This item unmark all currently marked sites across all sequences in the alignment grid.

Delete Gap-Only Sites: This item deletes gap-only sites (site columns containing gaps across all sequences) from the alignment grid. 

Auto-Fill Gaps: If this item is checked, then the Alignment Builder will ensure that all sequences in the alignment grid are the same length by padding shorter sequences with gaps at the end.