]> Merge two large overlapping nucleic acid sequences (EMBOSS) alignment:consensus http://bioweb.pasteur.fr/docs/EMBOSS/megamerger.html megamerger &emboss_init; input Input section asequence asequence -- DNA [single sequence] (-asequence) perl " -asequence=$value -sformat=fasta" 1 dna 8 seqfile perl 1 bsequence bsequence -- DNA [single sequence] (-bsequence) perl " -bsequence=$value -sformat=fasta" 2 dna 8 required Required section wordsize Word size (-wordsize) 20 perl " -wordsize=$value" 3 2 prefer Use the first sequence when there is a mismatch (-prefer) 0 perl ($value)? " -prefer" : "" 4 When a mismatch between the two sequence is discovered, one or other of the two sequences must be used to create the merged sequence over this mismatch region. The default action is to create the merged sequence using the sequence where the mismatch is closest to that sequence's centre. If this option is used, then the fist sequence (seqa) will always be used in preference to the other sequence when there is a mismatch. output Output section outseq outseq (-outseq) outseq.out perl " -outseq=$value" 5 seqfile perl 1 outseq_sformat Output format for: outseq fasta fasta gcg gcg phylip phylip embl embl swiss swiss ncbi ncbi nbrf nbrf genbank genbank ig ig codata codata strider strider acedb acedb staden staden text text fitch fitch msf msf clustal clustal phylip phylip phylip3 phylip3 asn1 asn1 fasta perl " -osformat=$value" 6 outfile outfile (-outfile) outfile.out perl " -outfile=$value" 7 auto perl " -auto -stdout" 8