Overview of all flags

Flags for input files:

Flag	Description
-similarity_score_file <filename>	file containing information about the type of alignment to be run
-fasta_file1 <filename>	file containing an amino acid sequence in fasta format
-fasta_file2 <filename>	file containing an amino acid sequence in fasta format
-msa_file1 <filename>	file containing a multiple sequence alignment, with entries all the same length
-msa_file2 <filename>	file containing a multiple sequence alignment, with entries all the same length

Note the following requirements:
-similarity_score_file must always be provided.

-fasta_file1 and -fasta_file2 must be provided together. The same is true for -msa_file1 and -msa_file2.

Flags for output files:

Flag	Description
-output_aligned_sequences <filename>	file to which the aligned amino acid sequences are printed
-output_aligned_profiles <filename>	file to which the aligned profile values are printed
-extract_from_MSA_sequences_with_ids [value1] [value2]	from each averaged multiple sequence alignment, a sequence is extracted. Value1 = i-th sequence from msa_file1. Value2 = j-th sequence from msa_file2
-output_extracted_sequences <filename>	file to which the sequences that are extracted from the averaged MSA are written

Gap penalty settings

You can choose one of the following gap penalty sets. A combination is not possible.

Flags for a set of 2 gap penalties:

Flag	Description
-gap_opening_penalty [value]	penalty for opening gaps
-gap_extension_penalty [value]	penalty for extending gaps

Flags for a set of 4 gap penalties:

Flag	Description
-gap_opening_penalty [value]	penalty for opening gaps within the sequence
-gap_extension_penalty [value]	penalty for extending gaps within the sequence
-termini_gap_opening_penalty [value]	additional penalty for opening gaps at the end of the sequence
-termini_gap_extension_penalty [value]	additional penalty for extending gaps at the end of the sequence

Flags for a set of 6 gap penalties:

Flag	Description
-thresholds_for_penalties [values]	defines a threshold according to which gap penalties are assigned
-below_threshold_gap_opening_penalty [value]	penalty for opening gaps opposite residues with a value below the threshold
-below_threshold_gap_extension_penalty [value]	penalty for extending gaps opposite residues with a value below the threshold
-above_threshold_gap_opening_penalty  [value]	penalty for opening gaps opposite residues with a value above the threshold
-above_threshold_gap_extension_penalty [value]	penalty for extending gaps opposite residues with a value above the threshold
-termini_gap_opening_penalty [value]	additional penalty for opening gaps at the end of the sequence
-termini_gap_extension_penalty [value]	additional penalty for extending gaps at the end of the sequence

Other flags

Flag	Description
-anchors <filename>	filename of the file containing a list of anchors, e.g. anchors.txt
-fraction_allowed_gaps [value]	columns of the MSA in which more than [value] positions are gaps are skipped and not considered in the alignment
-profile_gap_value_for_plotting [value]	define a value to be assigned to gaps in the output aligned profiles; default is ?0
-alignment_output_format	Formatting of the output alignment. Allowed types are ClustalW and fasta. By default, alignments are written in ClustalW format