# COMPALIGN(1) - man page online | user commands

Compare two multiple alignments.

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Mon, 01 Aug 2005 15:28:08 -0300

COMPALIGN(1) General Commands Manual COMPALIGN(1)NAMEcompalign - compare two multiple alignmentsSYNOPSIScompalign [-options] <trusted-alignment> <test-alignment>DESCRIPTIONcompalign 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 order. 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 alignment; 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.OPTIONSAvailable options: -h Print short help and usage info. -c Only compare under marked #=CS consensus structure. --informat <s> Specify that both alignments are in format <s> (MSF, for instance). --quiet Suppress verbose header (used in regression testing).SEE ALSOafetch(1), alistat(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), stranslate(1), weight(1).Mon, 01 Aug 2005 15:28:08 -0300 COMPALIGN(1)

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compalign(1) | referred by | afetch(1) | alistat(1) | compstruct(1) | revcomp(1) | seqsplit(1) | seqstat(1) | sfetch(1) | shuffle(1) | sindex(1) | sreformat(1) | stranslate(1) | weight(1) |

refer to | afetch(1) | alistat(1) | compstruct(1) | revcomp(1) | seqsplit(1) | seqstat(1) | sfetch(1) | shuffle(1) | sindex(1) | sreformat(1) | stranslate(1) | weight(1) |