Input File

www.cardiff.ac.uk/biosi/research/biosoft/

Mallard: Input File

When constructing an input file for the Mallard program ensure that:

A full-length Escherichia coli 16S rRNA gene sequence (such as U00096) is included as a reference sequence.
All sequences have

a sense orientation,
run from 5' to 3',
contain only valid base characters,
cover roughly the same region of the 16S rRNA gene,
are aligned with each other.

The resulting file should either be in Clustal format (with a .aln file ending) or Fasta format (with a .fas file ending).

Note...

When constructing an input file, consideration should also be given to the number of sequences and the phylogenetic diversity of the bacteria they represent. Bear in mind that anomalies are detected by the program through a series of comparative analyses amongst the sequences included within the file. So, try to avoid sequences that are too phylogenetically dissimilar, and try to include as many reliable sequences as possible, but no more than 1,000 as this will slow the program too much (program duration increases exponentially with sequence number).

As a rough guide, a good input file will be one that contains a reasonable number of sequences (say between 50-500), varying in overall phylogenetic difference by around 20% or less.

An example input file can be found here.