There are two types of command-line options: value options and flag options.
Value options
Value options are followed by the value of the given parameter, for example
–in filename.
Flag options
Flag options just stand for themselves, e.g. -quiet.
Option syntax
All options start with a dash (not two dashes!) followed by a long name.
There are no single-letter equivalents. Value options must be separated from
their values by white space in the command line. The order in which options are
given is irrelevant unless two options contradict, in which case the right-most
option silently wins.
Common options
| Option |
|
Values |
|
-in filename |
|
Sequences
to align. FASTA format. Any gaps in the sequences
are discarded before aligning. Default read from standard input.
|
|
-out filename |
|
Output file, default format is aligned FASTA. See also
output format options. Default write to
standard output.
|
|
-maxiters n |
|
Maximum
number of iterations to run. Default 16. Set to 2
for large datasets where refinement (iterations 3+) is too slow.
|
-in1 filename
-in2 filename |
|
Input
files for profile-profile alignment, i.e. to align
two multiple alignments to each other. Aligned FASTA format.
|
|
-profile |
|
Perform
profile-profile alignment, i.e. align two MSAs to
each other. Input files are -in1 and in2 (see above).
|
|
-quiet |
|
Do not
show progress messages.
|
|
-log filename |
|
Write
parameter information to the file.
|
|
-diags |
|
Use
diagonal optimization. This can significantly
improve speed with closely-related sequences. Disabled by default.
|
|
-maxhours h |
|
Maximim
time. If h hours have elpased, then complete the current
iteration and stop. Default no time limit.
|
|
-version |
|
Display
version and exit.
|
Complete option reference
Flag options
Value options
|