R"=====(
[b][u]trimAl [version].rev[revision] build [build]
[authors][r][b]
trimAl webpage: http://trimal.cgenomics.org

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, the last available version.

[u]Please cite:[r][b]

    trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
    Salvador Capella-Gutierrez; Jose M. Silla-Martinez; Toni Gabaldon.
    Bioinformatics 2009, 25:1972-1973.[r]


[b][u]Basic usage[r]
    trimal -in <inputfile> -out <outputfile> -(other options).


[b][u]Common options:[r]
For a complete list please see the User Guide or visit http://trimal.cgenomics.org

[b][u]Help Options[r]
    [b]--help[r]
        Print this information and show some examples.
    [b]--version[r]
        Print the trimAl version.
    [b]-v <n> / --verbose <n>[r]
        Specify the verbose level of the program.
        Available options: error / 3, warning / 2, info / 1, none / 0
        Default value: info / 1

[b][u]Input-Output Options[r]
    [b]-in <inputfile>[r]
        Input file in several formats.
        Available input formats: [iformat]

    [b]-formats <format1, ...>[r]
        Specify one or more formats to save the resulting MSA. Separated by spaces
        Combinations with specific format arguments (-fasta, -nexus, etc) is allowed.
        Available output formats: [oformat]

    [b]-out <outputfile>[r]
        Output path pattern. (default stdout).

         Following tags will be replaced if present on filename:
               [in]        -> Original filename without extension.
               [format]    -> Output's format name.
               [extension] -> Output's extension.
               [contig]    -> Contig name. Only applied if using VCF.

         This allows to store on several formats, without overriding the same file,
            as each format would replace the corresponding tags.
         It also allows to store the original filename of the input alignment into
            the result, allowing to reuse the same pattern for all inputs.
         In the case of the tag [contig] allows to store a MSA for each contig found.

         This can be used to store alignments in different folders, depending on the
            format, the input alignment, etc.
         Take in mind trimAl DOES NOT create new folders.

         Note: Format and extension may be the same depending on format.

         Examples:
            trimal -in ./ali1.fasta -out [in].clean.[extension]
                -> ./ali1.clean.fasta

            trimal -in ./alignment2.fasta -out [in].clean.[extension] -clustal
                -> ./file1.alignment2.clw

            trimal -in ./file1.fasta -out alig.[format].[extension] -formats clustal fasta pir
                -> ./alig.clustal.clw
                -> ./alig.pir.pir
                -> ./alig.fasta.fasta

            trimal -in file1.fasta -out ./[in]/trimmed.[format] -formats fasta
                -> ./file1/trimmed.fasta (ONLY if folder file1 already exists)

    [b]-lf / --listformats[r]
        List available formats to load from and save to.

[b][u]Report Output[r]
    [b]-htmlout <outputfile>[r]
        Get a summary of trimal's work in an HTML file.
    [b]-svgout <outputfile>[r]
        Get a summary of trimal's work in a SVG file.
    [b]-sgvstats <outputfile>[r]
        Get a summary of trimal's calculated stats in a SVG file.

    [b]-colnumbering[r]
        Get the relationship between the columns in the old and new alignment.

[b][u]Compare Set Options[r]
    [b]-compareset <inputfile>[r]
        Input list of paths for the files containing the alignments to compare.
    [b]-forceselect <inputfile>[r]
        Force selection of the given input file in the files comparison method.

[b][u]Backtranslation Options[r]
    [b]-backtrans <inputfile>[r]
        Use a Coding Sequences file to get a backtranslation for a given AA alignment
    [b]-ignorestopcodon[r]
        Ignore stop codons in the input coding sequences
    [b]-splitbystopcodon[r]
        Split input coding sequences up to first stop codon appearance

[b][u]Trimming Parameters[r]
    [b]--alternative_matrix degenerated_nt_identity[r]
        Specify the degenerated nt identity matrix as the similarity matrix to use.
        If a matrix is not specified, the best suited among a set will be selected.
    [b]-matrix <inpufile>[r]
        Input file for user-defined similarity matrix (default is Blosum62).
    [b]-block <n>[r]
        Minimum column block size to be kept in the trimmed alignment.
        Available with manual and automatic (gappyout) methods

    [b]-keepheader[r]
        Keep original sequence header including non-alphanumeric characters.
        Only available for input FASTA format files.
        (future versions will extend this feature)
    [b]-keepseqs[r]
        Keep sequences even if they are composed only by gaps.

    [b]-complementary[r]
        Get the complementary alignment in residues.
        Reverses the effect of residue trimming:
            All residues that were to be removed are kept and vice versa.
    [b]-complementaryseq[r]
        Get the complementary alignment in sequences.
        Reverses the effect of sequence trimming:
            All sequences that were to be removed are kept and vice versa.
            
    [b]-terminalonly[r]
        Only columns out of internal boundaries
        (first and last column without gaps) are
        candidates to be trimmed depending on the applied method

[b][u]Trimming Methods[r]

    [b][u]Manual Selection[r]

    [b]-selectcols { n,l,m-k }[r]
        Selection of columns to be removed from the alignment.
        Range: [0 - (Number of Columns - 1)]. (see User Guide).
    [b]-selectseqs { n,l,m-k }[r]
        Selection of sequences to be removed from the alignment.
        Range: [0 - (Number of Sequences - 1)]. (see User Guide).

    [b][u]Automated[r]

    [b]-nogaps[r]
        Remove all positions with gaps in the alignment.
    [b]-noallgaps[r]
        Remove columns composed only by gaps.

    [b]-noduplicateseqs[r]
        Removes sequences that are equal on the alignment.
        It will keep the latest sequence in the alignment.

    [b]-gappyout[r]
        Use automated selection on "gappyout" mode.
        This method only uses information based on gaps' distribution.
    [b]-strict[r]
        Use automated selection on "strict" mode.
    [b]-strictplus[r]
        Use automated selection on "strictplus" mode.
        Optimized for Neighbour Joining phylogenetic tree reconstruction.

    [b]-automated1[r]
        Use a heuristic selection of the automatic method
            based on similarity statistics. (see User Guide).
        Optimized for Maximum Likelihood phylogenetic tree reconstruction.

    [b]-clusters <n>[r]
        Get the most Nth representatives sequences from a given alignment.
        Range: [1 - (Number of sequences)]
    [b]-maxidentity <n>[r]
        Get the representatives sequences for a given identity threshold.
        Range: [0 - 1].


    [b][u]Overlap Trimming[r]
    Overlap is defined as having a gap in both positions,
        an indetermination in both positions, or a residue in both positions.
    It's main purpose is to remove sequences which share only a reduced region,
        whereas the other regions are not shared with the rest of sequences
        in the alignment and filled with gaps.
    Both arguments must be provided jointly.

        Ex: Sp8 may be removed from the alignment depending on the thresholds.

        Sp8    -----GLG-----------TKSD---NNNNNNNNNNNNNNNNWV-----------------
        Sp17   --FAYTAPDLLL-IGFLLKTV-ATFG-----------------DTWFQLWQGLDLNKMPVF
        Sp10   ------DPAVL--FVIMLGTI-TKFS-----------------SEWFFAWLGLEINMMVII
        Sp26   AAAAAAAAALLTYLGLFLGTDYENFA-----------------AAAANAWLGLEINMMAQI

    [b]-resoverlap <n>[r]
        Minimum overlap of a positions with other positions in the column
            to be considered a "good position".
        Range: [0 - 1]. (see User Guide).
    [b]-seqoverlap <n>[r]
        Minimum percentage of "good positions" that a sequence must have
            in order to be conserved.
        Range: [0 - 100](see User Guide).



    [b][u]Manual Trimming - Thresholds[r]

        [b]-gt -gapthreshold <n>[r]
            1 - (fraction of gaps in the column).
            Range: [0 - 1]
            Not compatible with -gat
        [b]-gat -gapabsolutethreshold <n>[r]
            Max number of gaps allowed on a column to keep it.
            Range: [0 - (number of sequences - 1)]
            Not compatible with -gt
        [b]-st -simthreshold <n>[r]
            Minimum average similarity required.
            Range: [0 - 1]
        [b]-ct -conthreshold <n>[r]
            Minimum consistency value required.
            Range: [0 - 1]
        [b]-cons <n>[r]
            Minimum percentage of positions
                in the original alignment to conserve.
            Range: [0 - 100]

[b][u]Half Windows[r]
Half window size, score of position i is the average of the window (i - n) to (i + n).
Only compatible with manual methods.

    [b]-w <n>[r]
        (half) General window size, applied to all stats.
            Not compatible with specific sizes.
    [b]-gw <n>[r]
        (half) Window size applied to Gaps.
    [b]-sw <n>[r]
        (half) Window size applied to Similarity.
    [b]-cw <n>[r]
        (half) Window size applied to Consistency.

[b][u]Statistics Output[r]
Statistics to be calculated and outputted by trimAl

    [b]-sgc[r]
        Print gap scores for each column in the input alignment.
    [b]-sgt[r]
        Print accumulated gap scores for the input alignment.
    [b]-ssc[r]
        Print similarity scores for each column in the input alignment.
    [b]-sst[r]
        Print accumulated similarity scores for the input alignment.
    [b]-sfc[r]
        Print sum-of-pairs scores for each column from the selected alignment
    [b]-sft[r]
        Print accumulated sum-of-pairs scores for the selected alignment
    [b]-sident[r]
        Print identity scores for all sequences in the input alignment.
        (see User Guide).
    [b]-soverlap[r]
        Print overlap scores matrix for all sequences in the input alignment.
        (see User Guide).

[b][u]NGS Support - VCF SNP MSA creator[r]
Suport for VCF files. Providing a reference genome,
    and one or more VCF, multiple MSA are created.
One MSA for each contig present on the whole VCF-dataset.
Each MSA contains the reference sequence
    and a sequence for each donor, with their SNP applied.

    [b]-vcf <inputfile, ...>[r]
        Specify one or more VCF files to produce MSAs
            using the input file (-in <n>) as reference genome.
        It will produce a MSA for each sequence on the original alignment.
        Each MSA will contain the same number of sequences:
            Number of donors + 1 (reference).

        If output file is given, it is recommended to use
            the tag "[contig]" in the filename.
            (See [b]-out[r] explanation)
        Otherwise, the alignments will be stacked
            one upon another on the same file.
        This is valid on formats like fasta or pir,
            but will yield a non-valid file for other formats, such as clustal.

        If no output file pattern is given (-out <outputfile>)
            or it doesn't contain the tag "[contig]",
            the sequences names will have the name of their contig prepended.

    [b]-minquality <n>[r]
        Specify the min quality of a SNP in VCF to apply it.
        Only valid in combination with -vcf.

    [b]-mincoverage <n>[r]
        Specify the min coverage of a SNP in VCF to apply it.
        Only valid in combination with -vcf.

    [b]-ignoreFilter[r]
        Ignore vcf-filtered variants in VCF.
        Only valid in combination with -vcf.
        Still applies min-quality and min-coverage when provided.

[b][u]Legacy Options[r]
These options are included for back-compatibility with older versions of trimAl.
New formats will not be added to this list of output format arguments.
The new formats argument "-formats <format1, format2, etc>" should be used instead.

    [b]-nbrf[r]
        Output file in NBRF/PIR format
    [b]-mega[r]
        Output file in MEGA format
    [b]-nexus[r]
        Output file in NEXUS format
    [b]-clustal[r]
        Output file in CLUSTAL format
    [b]-fasta[r]
        Output file in FASTA format
    [b]-fasta_m10[r]
        Output file in FASTA format.
        Sequences name length up to 10 characters.
    [b]-phylip[r]
        Output file in PHYLIP/PHYLIP4 format
    [b]-phylip_m10[r]
        Output file in PHYLIP/PHYLIP4 format.
        Sequences name length up to 10 characters.
    [b]-phylip_paml[r]
        Output file in PHYLIP format compatible with PAML
    [b]-phylip_paml_m10[r]
        Output file in PHYLIP format compatible with PAML.
        Sequences name length up to 10 characters.
    [b]-phylip3.2[r]
        Output file in PHYLIP3.2 format
    [b]-phylip3.2_m10[r]
        Output file in PHYLIP3.2 format.
        Sequences name length up to 10 characters.

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