4.11 BppAlnScore: Bio++ Alignment Scoring

This program compares two alignments and computes column scores. Scores are output to a text file, and/or can be used to generate a site selection, to be output in a mase file.

The two input alignments are specified using the input.sequences procedures (see Sequences), with suffixes “.test” for the first one, and “.ref” for the second. Scores will be computed for each column of the “.test” alignment.

Two scores are computed, following work by Thompson (1999):

column score (CS)

is 1 if the column is found in the reference alignment, 0 otherwise.

sum-of-pairs score (SPS)

is the proportion of pairs of residues which are also aligned in the reference alignment.

Specific options:

output.scores = {path}

A text file where scores can be written, one row per column. If set to 'none', no file will be produced.

output.mase = {path}

If not 'none', a Mase alignment will be generated, as a copy of the “.test” input alignment, with two sites selections names CS and SPS.

output.sps_thresholds = {float}

The threshold to use for generating the site selection based on SPS score. All positions with at least the threshold value will be included in the selection.

score.word_size = {int>0}

If alignment is for a word alphabet (typically codons), the word size can be specified in order to produce a compatible site selection. Please note that in this case, the alignment must not be loaded with the world alphabet, but the corresponding letter alphabet.

score.phase = {int>0|chars}

Eather a number (1-based) stating the starting position for words, or the starting word. In this latter case, the first occurrence of the word in all sequences will be used to determine the phase.