This is the command compalign that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
compalign - compare two multiple alignments
compalign [-options] <trusted-alignment> <test-alignment>
compalign calculates the fractional "identity" between the trusted alignment and the test
alignment. The two files must contain exactly the same sequences, in exactly the same
The identity of the multiple sequence alignments is defined as the averaged identity over
all N(N-1)/2 pairwise alignments.
The fractional identity of two sets of pairwise alignments is in turn defined as follows
(for aligned known sequences k1 and k2, and aligned test sequences t1 and t2):
matched columns / total columns
where total columns = the total number of columns in which there is
a valid (nongap) symbol in k1 or k2;
matched columns = the number of columns in which one of the
following is true:
k1 and k2 both have valid symbols at a given column; t1 and t2
have the same symbols aligned in a column of the t1/t2
k1 has a symbol aligned to a gap in k2; that symbol in t1 is
also aligned to a gap;
k2 has a symbol aligned to a gap in k1; that symbol in t2 is
also aligned to a gap.
Because scores for all possible pairs are calculated, the algorithm is of order (N^2)L for
N sequences of length L; large sequence sets will take a while.
-h Print short help and usage info.
-c Only compare under marked #=CS consensus structure.
Specify that both alignments are in format <s> (MSF, for instance).
Suppress verbose header (used in regression testing).
Use compalign online using onworks.net services