If a residue in the test sequence was aligned to a non-gap position in the reference alignment, it is correct in the output alignment if it is aligned to that same position, and incorrect otherwise.
In addition, we have a weak anchoring option, where consistent anchor points are only used to constraint the output alignment, but are not necessarily aligned to each other.
Submitted nucleic acid sequences or protein sequences in FASTA format are computed for the output alignment in PHYLIP format using ClustalW; a query initiated in a pre-aligned file in PHYLIP format by other sequence align tools disregards this procedure.
We did not use 'Palindrome' program developed by EMBOSS, since the output did not give the length of sequence and was difficult to make out whether the output alignment is a palindrome or IR sequence.
The default output alignment format is SAM (Sequence Alignment/Map format).
The output alignment files in SAM format were further processed using SAMtools [ 43].
Common formats for input and output alignment files are handled: Fasta, Phylip [ 17], Must [ 18] or Nexus [ 19].
Briefly, the contrast setting determines how many of the most discriminating pattern residues are highlighted in the output alignment.
The output alignment was manually refined using GeneDoc 2.6 [ 62] and this new alignment was used to build a neighbor-joining tree with 1000 bootstrap replicates in ClustalX2.
