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Open a new alignment.
Save the currently selected data item of the tree view to a file.
Remove the currently selected data item.
Rename the current data item.
View the current data item in a viewer. In case of tree viewing Profiles are marked by "Pi" (profile generated by identity threshold), "Pb" (profiles generated by bootstrap threshold) and "Po" (old profile generated in a previous iteration)
Show available transform actions.

Data Items

Represents a RNA/DNA alignment. You can perform Profile Neighbour Joining, Bootstrap and Distance Calculation on this data type.
Represents a set of RNA/DNA alignments after Bootstrap. You can perform Distance Calculation on this data type.
Represents a RNA/DNA structure alignment. You can perform Profile Neighbour Joining, Bootstrap and Distance Calculation on this data type.
Represents a set of RNA/DNA structure alignments after Bootstrap. You can perform Distance Calculation on this data type.
Represents a Protein alignment. You can perform Profile Neighbour Joining, Bootstrap and Distance Calculation on this data type.
Represents a set of Protein alignments after Bootstrap. You can perform Distance Calculation on this data type.
A resulting distance matrix after performing a Distance Calculation on a single alignment. You can perform Neighbour Joining on this data type.
A resulting set of distance matrices after performing a Distance Calculation on a set of alignments. You can perform Neighbour Joining on this data type.
Represents a phylogenetic tree which can be a result of Consensus operation. If you perform Neighbour Joining on a single distance matrix, then this data type is the result of it.
Represents a set of phylogenetic trees which can be a result of Neighbour Joining after performing Neighbour Joining on a set of distance matrices. It these trees are the result of Neihghbour Joining you can perform Consensus on them.
This is the resulting data type of a Profile Neighbour Joining operation, which represents the resulting trees.

Transform Actions

Profile Neighbour Joining operation.
Bootstrap operation.
Distance operation.
Neighbour Joining operation.
Consensus operation.

Expert Mode

ProfDistS offers in its Profile-Neighbour-Joining-Dialog an Expert Mode button which shows more options. There the user can define two thresholds used for profile generation:
  • Profiles are generated due to the chosen level of sequence identity (%)
  • Profiles are generated due to the chosen level of bootstrap support values
Furthermore the user can choose can between automatic and manual profile generation modi.