PID calculation for tree calculation includes gapped columns in the alignment length used for %age calculation

The PID calculated for pairs of sequences always takes the length of the longest sequence string as the denominator for calculating the percentage identity, regardless of the presence of affine gaps (ie gaps in all rows at a particular column of the alignment). This means that the dissimilarity values calculated for a particular alignment may be lower than expected if the alignment includes affine gaps, since these will be considered matches under the PID calculation.