Calculate base frequencies and/or a base frequency filter.
Open Config/Filter to define how the filter will be created:
Define the alignment range, for which the filter shall be generated using the input fields 'Start at column' and 'Stop at column'. Columns outside that range will get filtered, i.e. the generated filter will contain '0'.
Define the similarity range, which will lead to a '1' in the resulting base frequency filter, by specifying the lower and upper percentage in the input field 'Minimal similarity' and 'Maximal similarity'. Similarity values outside that range will lead to '0' in the generated base frequency filter and will as well not be exported as base frequencies. (Note: It's not necessary to re-calculate, when you change this value)
For non-regular sequence characters (gaps, ambiguity codes and lowercase characters) you may define how the frequency calculation acts, by setting their toggles to one of the following values:
don't count (ignore)
The corresponding characters are ignored (as if they were not present).
if occurs most often => forget whole column
If the corresponding character(s) occur(s) more often than any other regular sequence character, then skip column, i.e. write '0' to filter.
if occurs => forget whole column
If (one of) the corresponding character(s) occurs, then skip the column, i.e. write '0' to filter.
count, but do NOT use as maximum
The corresponding characters are counted like regular sequence characters, but never interpreted as "being the most homologous character". Compared with 'don't count' it will result in lower base frequencies, cause the overall number of characters occurring per column will be higher.
treat as regular character
This is only applicable to 'ambiguity codes'. Treats ambiguity codes like regular sequence characters. (Note: 'treat as uppercase char' setting for lowercase characters affects ambiguity codes as well, if treated as regular characters)
treat as uppercase char
This is only applicable to 'lowercase chars'. Simply treat regular lowercase sequence characters like uppercase characters.
Press 'Calculate/Column Filter' to calculate the base frequencies.
When calculated, three lines will appear below your sequences in the main window. Reading the columns of these 3 lines from top to bottom, they mark completely filtered columns by 'XXX' and else show the frequency of the most frequent base in percent.
The color of each column indicates whether the frequency will be exported and respectively whether the column will be '0' or '1' in the base frequency filter.
If pleased with the results, either export detailed base frequencies via 'File/Export frequencies' or export a base frequency filter via 'File/Export filter'.