Command line options
Sequences
A pair of sequences, or one/two database files are mandatory parameters. Use one of the following option combinations:
Actual sequences given directly in the command line
- -s1 <seq>
- First sequence. For example: "AGN"
- -s2 <seq>
- Second sequence. For example: "QET"
One database file
All possible pairs of sequences from the database will be aligned.
- -b,--database <file path>
- Path to the database (multifasta format by default).
Two database files
All possible pairs of sequences, one from each database, will be aligned.
- -S1 <file path>
- Path to the first database (multifasta format by default)
- -S2 <file path>
- Path to the second database (multifasta format by default)
Other sequence-related parameters
- -f,--database-format <s|f|fd>
- Database format. Possible values: s (=simple file, one sequence per row, no headers), f (=fasta file), fd (=directory with fasta files). Default: f.
- -filter,--database-filter-string <string>
- Select those entries in the database whose identifier contains this string (regular expressions not yet supported).
- -st <dna|rna|prot|auto>
- Sequence type; possible values: dna, rna, prot, auto (=autodetection of the sequence type). Default: auto.
- -gx,--expand
- To be used with DNA/RNA input sequences. If present, genomic sequences are expanded into the complete back-translation graphs of the encoded protein.
- -z,--compression
- Compression of back-translation graphs using IUPAC nucleotide ambiguity codes. Default: false; becomes true if this option is present.
Alignment parameters
General
- -a,--alignment-type <g|l|o>
- Alignment type; values: g (=global), l (=local), o (=overlap). Default: l
- -G,--gapping-type <l|a|f>
- Gapping type; values: l (=linear), a (=affine), f(=frameshift/codon). Default: f
- -fs,--allowed-frameshifts <number>
- Number of allowed frameshifts. Default: 4
- -rc,--reverse-complementary
- By default, the two sequences are aligned in the forward sense. If this parameter is present, the first sequence is also aligned with reverse complementary of the second.
- -rcOnly,--reverse-complementary-only
- By default, the two sequences are aligned in the forward sense. If this parameter is present, the first sequence is only aligned with reverse complementary of the second.
Scores
- -sm,--score-matrix <file>
- Nucleotide pair score matrix to use; if provided, the parameters m, x, tx are ignored. See also: translation dependent score matrices.
- -m,--match <number>
- Match score Default: 1.
- -t,--transition <number>
- Transition mutation mismatch score (default: the mismatch score)
- -x,--mismatch <number>
- Mismatch score (transversion mutation). Default: -1.
Gap penalties
- -c,--codon-gap-penalty <number>
- Penalty for full codon gaps, to be used with alignments having a frameshift/codon gapping type. Default: -3.
- -ce,--codon-gap-extension-penalty <number>
- Penalty for extending full codon gaps, to be used with alignments having a frameshift/codon gapping type. Default: -3.
- -d,--gap-opening <number>
- Affine gap opening penalty. For alignments having a frameshift/codon gapping type, this is the penalty used for opening frameshift gaps. Default: -4.
- -e,--gap-extension <number>
- Affine gap extension penalty. For alignments having a frameshift/codon gapping type, this is the penalty used for extending frameshift gaps. Default: -1.
- -g,--lgap <number>
- Linear gap penalty. Default: -1.
Evaluation
- -eP,--estim-params-file <file path>
- Path of the file that contains the parameters used to determine the score's statistical significance.
- -mev,--max-evalue <number>
- Maximum accepted e-value for alignments to be considered significant. Default: 0.001.
Output
- -o,--output <file path>
- Output all performed alignments to a file. If this parameter is not present, only selected alignments will be preinted.
- -os,--selection-output <file path>
- Output selected alignments (i.e. with an e-value lower than the given threshold) to a file. If this parameter is not present, the selected alignments are printed to stdout.
- -xml,--xml-output <file path>
- Output to a file in xml format.
- -FS,--frameshifts-only
- Only print alignments that contain at least a frameshift.
Other
- -h,--help
- Prints help and exits.
- -q,--quiet
- Do not print any messages.
- -v,--verbose
- Print more messages.
- -P,--progress
- Prints progress bar.