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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.