ALIGNALIGN(1) User Commands ALIGNALIGN(1) NAME alignalign - align a pair of multiple sequence alignments SYNOPSIS alignalign <-a alignment file> <-b alignment file> [OPTION]... DESCRIPTION OPTIONS all options are order independent -a file use file, in fasta format, as the first alignment -b file use file, in fasta format, as the first alignment -c file, -costmatrix file use substitution costs contained in file -d n use gap open cost n -e n, -extension n use gap extention cost n -g n1 n2, -gap n1 n2 use gap open cost n1 and gap extension cost n2 -f filename, -f2c filename simply convert the input file filename from FASTA format to CLUSTAL format -h, -help print this document -j filename, -justscore filename calculate the SP score for the input file filename -k use the pessimistic heuristic for gap counts (default is to use exact counts - slower) -o file, -outfile file write output alignment to file -p do *not* print the solution alignment -q, -quiet do not print summary data -s, -space use the space-optimized version (at the expense of computation time) -t, -time use the time-optimized version (at the expense of computation space) -v, -verbose print summary data (default) -w n -width n format output alignment into blocks of n columns -x if printing the solution alignment, print in FASTA format -y if printing the solution alignment, print in CLUSTAL format (default) BUILD type "make" at the command prompt alignalign-1.0.0 17 May 2007