Full package name: mesquite.align.AlignToDropped.AlignToDropped Duty: INIT Assistant for Data Window (mesquite.lib.duties.DataWindowAssistantI)
Module Explanation
Supplies an alignment tool that can be used on a set of sequences. Sequences dropped by this tool on another sequence will be aligned to that other sequence (pairwise).
Author(s): Wayne P. Maddison and David R. Maddison
Version 3.70
Commands of Align To Dropped
toggleAllowNewGaps
Explanation: Toggles whether the new gaps can be introduced into one or the other sequence.
Parameters: [on; off]
gapCosts
Explanation: Allows one to specify gap opening and extension costs.
Parameters: [open; extend]
subCosts
Explanation: Allows one to specify substitution costs.
Parameters: [matrix of costs]
alignDropTouched
Explanation: AlignToDropped tool touched on row.
Parameters: [column touched] [row touched]
alignDropDragged
Explanation: AlignToDropped tool dragged.
Parameters: [column dragged] [row dragged]
alignDropDropped
Explanation: AlignToDropped tool dropped.
Parameters: [column dropped] [row dropped]
toggleWarnCheckSum
Explanation: Toggles whether the data integrity is checked or not after each use.
Parameters: [on; off]
toggleAllowNewGaps
Explanation: Toggles whether the new gaps can be introduced into one or the other sequence.
Parameters: [on; off]
toggleReverseComplementIfNecessary
Explanation: Toggles whether each sequence to be aligned should check to see if it needs to be reverse complemented before aligning.
Parameters: [on; off]
saveDefaults
Explanation: Saves current settings as defaults
Parameters: [none]
toggleIgnoreFileSettings
Explanation: Specifies whether or not file settings are to be ignored
Parameters: [on; off]
gapCosts
Explanation: Allows one to specify gap opening and extension costs.
Parameters: [open; extend]
subCosts
Explanation: Allows one to specify substitution costs.
