This algorithm is for counting of nucleotide substitutions number in previously aligned nucleotide sequences (up to 100 sequences, 4 000 nucleotides in length).
The direction of nucleotide substitutions is estimated by the "quantitative" way: from the nucleotide in consensus sequence to the nucleotide (nucleotides) which are found in this site less frequently.
There are two ways of nucleotide substitutions number counting in this algorithm. Substitutions are counted "per site" and "per nucleotide". Counting "per site" means that common nucleotide substitutions observed in this site in several sequences are due to a single substitution happened ones in the common predecessor of all mutated sequences. Counting "per nucleotide" means that common nucleotide substitutions occurred independently in each of all mutated sequences.
Results of the counting "per site" and "per nucleotide" will appear in two tables on "gene1" list several seconds after the entrance of your sequences in cells on "sequences" list.
Nucleotide content distribution between codon positions of all inserted sequences is also calculated by "VVK Consensus". Results of this counting can be found on "content" list.
WARNING: do not use "-" symbol to indicate gaps. Ms Excel is working badly with this symbol. Better replace it by any letter different from "A", "T", "G" and "C".
Khrustalev V.V., Barkovsky E.V. Unusual nucleotide content of Rubella virus genome as a consequence of biased RNA-editing: comparison with Alphaviruses // International Journal of Bioinformatics Research and Applications – 2011. – Vol.7. – Issue 1. – P.82-100.