Sonnhammer, E. L. & Hollich, V. Scoredist: a simple and robust protein sequence distance estimator.
Alignment, classification, sequence distance calculation, OTU clustering, phylogenetic tree construction, and calculation of among-sample phylogenetic distances were done using the software package mothur60,61.
The protein sequence similarity was converted from the global sequence distance obtained by ClustalO [14].
The transition between single step long-range tunneling and multistep hopping transport in DNA electron transfer depends on a myriad of factors including sequence, distance, conformation, solvation and, consequently, hole state energetics.
For all considered sequence distance measures we observed the following pattern among the V3 loop sequences.
This number is referred to as the sequence distance or 1D distance.
On average, the codon sequence distance between glutamic acid and glycine is 1.75 nucleotides.
Thus, FastGroup at 1.5% sequence distance can be compared to complete linkage and ESPRIT at 3%.
The sequence distance between specimens in different families was always great than 12% (mean 23.67%, range 12.2 36.7%).
First, the fraction of unique functions increases with increasing sequence distance of the neighborhood centers G1 and G2 (Figure 4b).
Mean K2P sequence distance between congeneric species (10.81%) was approximately 26-fold higher than within species variation (0.42%, uncorrected).
