Select the "Show advanced options" Button at the top to gain access to
the you-may-now-shoot-yourself-in-the-foot-severely dialog window.
Don't be surprised if the graph aligner crashes after you entered silly
values here. No sanity check of your options is done.
Turn check:
If selected (default) sequences will be automatically reversed
and/or complemented if this will likely improve the alignment.
Realign:
If selected, the sequence itself is excluded from the result of
the executed PT-Server family search. If deselected, the alignment
of an identical sequence found by the PT-Server is copied.
Load reference sequence from PT Server:
Do not read alignment data from your current database, but from the
database the PT-Server was built from. This makes starting the
graph aligner much slower, but allows you to align against external
databases or PT-Servers with different sequence names than your
current database.
(Copy and) mark sequence used as reference:
Mark the sequences that were used as a reference during alignment.
This allows you to easily load them into the editor to review the
decisions made by the graph aligner.
If you also selected the "Load reference" option, sequences will be
copied into your current database prior to being marked.
Gap insertion/extension penalties: (default is 5/2)
You can change the penalties associated with opening and extending
gaps.
Family search min/min_score/max: (default 15,0.7,40)
The first value tells the graph aligner how many sequences it should
try to always use. The second value determines the minimal identity
with the target sequence additional reference sequences should have.
The third value selects the maximal number of sequences to be used
as a reference.
Use at least X sequences with at least Y bases: (SSU-default is 1, 1400)
This option allows you to require that the reference include X
sequences of a length larger than or equal to Y.
Aligner threads / Queue size:
Up to 4 threads can be used to align simultaneously. If your workstation
sports multiple CPUs this will speed up alignment of many sequences.
Increase the size of the buffer between the graph aligner components to
about 15 when using 4 threads.
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