input.sequence.file={path}The sequence file to use. Depending on the program, these sequences have or do not have to be aligned.
input.sequence.format = {sequence format description}The sequence file format.
input.site.selection = {list of integers}Will only consider sites in the given list of positions, in extended format : positions separated with ",", and "i-j" for all positions between i and j, included.
input.site.selection = {Sample(n={integer} [, replace={true}])}Will consider {n} random sites, with optional replacement.
Since Bio++ Program Suite version 0.4.0, the format description uses the keyval syntax. The format is a function, with optional parameters:
Fasta(extended={bool}, strictNames={bool})The fasta format.
The argument extended, default to ’no’, allows to enable the
HUPO-PSI extension of the format.
The argument strict_names, default to ’no’, specifies that
only the first word in the fasta header is used as a sequence names,
the rest of the header being considered as comments.
Mase(siteSelection={chars})The Mase format (as read by Seaview and Phylo_win for instance), with an optional site selection name.
Phylip(order={interleaved|sequential}, type={classic|extended}, split={spaces|tab})The Phylip format, with several variations.
The argument order distinguishes between sequential and
interleaved format, while the option type distinguished
between the plain old Phylip format and the more recent extension
allowing for sequence names longer than 10 characters, as understood
by PAML and PhyML.
Finally, the split argument specifies the type of character
that separates the sequence name from the sequence content. The
conventional option is to use one (classic) or more (extended) spaces,
but tabs can also be used instead.
Clustal(extraSpaces={int})The Clustal format.
In its basic set up, sequence names do not have space characters, and
one space splits the sequence content from its name. The parser can
however be configured to allow for spaces in the sequence names,
providing a minimum number of space characters is used to split the
content from the name. Setting extraSpaces to 5 for
instance, the sequences are expected to be at least 6 spaces away for
their names.
Dcse()The DCSE alignment format. The secondary structure annotation will be ignored.
Nexus()The Nexus alignment format. Only very basic support is provided.
For programs that do not require the sequences to be aligned, the following formats are also available:
GenBank()Very basic support: only retrieves the sequence content for now, all features are ignored.
Basic operations can be performed on the sequences:
input.sequence.sites_to_use = {all|nogap|complete}This option only works if the program requires an alignment. Tells which sites to use. The nogap option removes all sites containing at least one gap, and the complete option removes all sites containing at least one gap or one generic character, as ’X’ for instance.
input.sequence.remove_stop_codons = {boolean}This option only works if the alphabet is a codon alphabet. Removes the sites where there is a stop codon (default: ’yes’).
input.sequence.max_gap_allowed=100%This option only works if the program requires an alignment. Only works when the all option is selected. It specifies the maximum amount of gap allowed per site, as a number of sequence or a percentage. Sites not matching the criterion will not be included in the analysis, but the original site numbering will be used in the output files (if relevant).
input.sequence.max_unresolved_allowed=100%This option only works if the program requires an alignment. Only works when the all option is selected. It specifies the maximum amount of unresolved states per site, as a number of sequence or a percentage. Sites not matching the criterion will not be included in the analysis, but the original site numbering will be used in the output files (if relevant).