Create multiple alignments of amino acid sequences according to the method of Edgar.

seqaln.pair(aln, ...)



a sequence character matrix, as obtained from seqbind, or an alignment list object as obtained from read.fasta.


additional arguments for the function seqaln.


This function is intended for the alignment of identical sequences only. For standard alignment see the related function seqaln.

This function is useful for determining the equivalences between sequences and structures. For example in aligning a PDB sequence to an existing multiple sequence alignment, where one would first mask the alignment sequences and then run the alignment to determine equivalences.


A list with two components:


an alignment character matrix with a row per sequence and a column per equivalent aminoacid/nucleotide.


sequence names as identifers.


Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

‘MUSCLE’ is the work of Edgar: Edgar (2004) Nuc. Acid. Res. 32, 1792--1797.

Full details of the ‘MUSCLE’ algorithm, along with download and installation instructions can be obtained from:


Barry Grant


A system call is made to the ‘MUSCLE’ program, which must be installed on your system and in the search path for executables.

See also


## NOTE: FOLLOWING EXAMPLE NEEDS MUSCLE INSTALLED if(check.utility("muscle")) { ##- Aligning a PDB sequence to an existing sequence alignment ##- Simple example aln <- seqbind(c("X","C","X","X","A","G","K"), c("C","-","A","X","G","X","X","K")) seqaln.pair(aln, outfile = tempfile()) }
#> 1 10 #> seq1 XCXXA-G--K #> seq2 -C--AXGXXK #> ^*^^*^*^^* #> 1 10 #> #> Call: #> seqaln.pair(aln = aln, outfile = tempfile()) #> #> Class: #> fasta #> #> Alignment dimensions: #> 2 sequence rows; 10 position columns (4 non-gap, 6 gap) #> #> + attr: id, ali, call