analyser

The analyser program does not require any control file. To use analyser, type at the command-line:
analyser or
analyser data-file
where data-file is a file following the data file format. The analyser program needs you to provide the fields usually used in the DATAFILE block in order to parse your sequences. Once it is done you will be prompted for the class to check if the data file contains heterogeneous sites and analyser will require a ``.lump'' file.

The ``.lump'' file is used:

1. to match sites to a given state, e.g., indels(-) and purine(R) can be lumped to an ambiguity state(X).
2. to choose the state(s) used for the cut-off (see below).

Two ``.lump'' files are provided, data/dna.lump and data/rna.lump. The first one is used with single nucleotide, ambiguity -- i.e., -, R, Y and X -- are lumped in a state X used for the cut-off. The second one is used with paired sites. mismatches -- e.g., AC, UU, ...-- are lumped into the single state MM and ambiguity -- e.g., C-, UR, ...-- are lumped into the state XX. Both states are used for the cut-off.

Once the ``.lump'' file is provided, analyser outputs statistics for each state and requires a value for the cut-off (between 0 and 1.0). For each site the frequencies of ``cut-off states'' is computed and the sites above the cut-off threshold provided are displayed on the screen.