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C<coverage_mul> parameter of the C<config> file.

Then comes the alignment itself. With nucleotide C<banks>, both C<BLAST> and
C<exonerate> aligners are available, whereas only C<BLAST> can be used with
protein C<banks>. The preferred aligner can be specified using the C<aligner>
parameter of the C<config> file.

The C<BLAST> aligner has been much improved with respect to the aligner of the
original C<forty>. It extracts all the HSPs for the selected template(s) from
the XML C<BLAST> report and uses them as guides for integrating the orthologue
fragments into the MSA. Then, once all fragments have been integrated for all
candidate organisms, it merges them into a single contiguous sequence per
orthologue. When fragments overlap, the merger gives precedence to the fragments
corresponding to the highest-scoring templates and HSPs.

When the new C<exonerate> aligner is preferred, only the longest selected
template is used. In most cases, the orthologue can be aligned as a single large
fragment. If not, C<42> emits different types of warnings depending on the exact
issue. In worst cases (e.g., C<exonerate> crashing), the orthologue cannot be
integrated, often due to structural rearrangements between the orthologue and
the template. To avoid discarding the orthologue in such cases, one can enable
C<BLAST> as a fall-back for exonerate failures by setting the C<aligner>
parameter to C<exoblast>.

Aligned orthologues are integrated into the MSA all together at the end of the
file but in the following arrangement: first by family, then by candidate
organism and then by accession. Contaminants are interspersed with genuine
orthologues but can be easily identified thanks to their tag (C<c#>).

lib/Bio/MUST/Apps/FortyTwo/Manual.pod  view on Meta::CPAN

either already present in the MSA or that are listed in the C<NON> counterpart
of the MSA. C<NON> files are a bit like C<PARA> files (non-aligned sequences in
C<FASTA> format) except that matches must be exact. Finally, when a newly added
orthologue includes a sequence already present in the MSA for the same organism,
the latter can be either kept or removed, depending on the value of the
parameter C<ali_keep_lengthened_seqs> in the C<config> file.

=head3 C<#NEW#> tags

All newly added orthologues are tagged by a specific C<#NEW#> suffix. This tag
helps C<42> to organize the post-processing of new sequences (e.g., fragment
merging and redundancy detection) but is also useful for the end-user to
identify which sequences have been added by C<42>. Therefore any preexisting
C<#NEW#> tag is cleared when C<42> starts processing a MSA.

While automatic untagging can be disabled via the parameter
C<ali_keep_old_new_tags> in the C<config> file, one should note that such
preexisting new sequences are basically invisible to C<42>. This means that they
will not be chosen as queries for mining transcriptomes nor as templates for
aligning additional new orthologues. Moreover they will not be considered for
taxonomic analyses. That is why the recommended approach is to let this