trimAl v1.2 command line version

   trimal -in <inputfile> -out <outputfile> -(other options) 

   -h                       Print this information and show some examples.
   --version                Print the trimAl version.

   -in <inputfile>          Input file in several formats (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip).
   -compareset <inputfile>  Input list of paths for the files containing the alignments to compare.
   -matrix <inpufile>       Input file for user-defined similarity matrix (default is Blosum62).

   -out <outputfile>        Output alignment in the same input format (default stdout). (default input format)
   -htmlout <outputfile>    Get a summary of trimal's work in an HTML file.

   -clustal                 Output file in CLUSTAL format
   -fasta                   Output file in FASTA format
   -nbrf                    Output file in NBRF/PIR format
   -nexus                   Output file in NEXUS format
   -mega                    Output file in MEGA format
   -phylip3.2               Output file in PHYLIP3.2 format
   -phylip                  Output file in PHYLIP/PHYLIP4 format

   -complementary           Get the complementary alignment.
   -colnumbering            Get the relationship between the columns in the old and new alignment.

   -select { n,l,m-k }      Selection of columns to be removed from the alignment. (see User Guide).
   -gt -gapthreshold <n>    1 - (fraction of sequences with a gap allowed).
   -st -simthreshold <n>    Minimum average similarity allowed.
   -ct -conthreshold <n>    Minimum consistency value allowed.
   -cons <n>                Minimum percentage of the positions in the original alignment to conserve.

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

   -gappyout                Use automatic selection on "gappyout" mode. This method only uses information based on gaps' distribution. (see User Guide).
   -strict                  Use automatic selection on "strict" mode. (see User Guide).
   -strictplus              Use automatic selection on "strictplus" mode. (see User Guide).

   -automated1              Use a heuristic selection of the automatic method based on similarity statistics. (see User Guide).

   -resoverlap              Minimum overlap of a positions with other positions in the column to be considered a "good position". (see User Guide).
   -seqoverlap              Minimum percentage of "good positions" that a sequence must have in order to be conserved. (see User Guide).

   -w <n>                   (half) Window size, score of position i is the average of the window (i - n) to (i + n).
   -gw <n>                  (half) Window size only applies to statistics/methods based on Gaps.
   -sw <n>                  (half) Window size only applies to statistics/methods based on Similarity.
   -cw <n>                  (half) Window size only applies to statistics/methods based on Consistency.

   -sgc                     Print gap percentage count for columns in the input alignment.
   -sgt                     Print accumulated gap percentage count.
   -scc                     Print conservation values for columns in the input alignment.
   -sct                     Print accumulated conservation values count.
   -sfc                     Print compare values for columns in the selected alignment from compare files method.
   -sft                     Print accumulated compare values count for the selected alignment from compare files method.
   -sident                  Print identity statistics for all sequences in the alignemnt. (see User Guide).

1) Removes all positions in the alignment with gaps in 10% or more of the sequences, unless this leaves less than 60%. In such case, print the 60% best (with less gaps) positions.

   trimal -in <inputfile> -out <outputfile> -gt 0.9 -cons 60 

2) As above but, the gap percentage is averaged over a window starting 3 positions before and ending 3 positions after the column.

   trimal -in <inputfile> -out <outputfile> -gt 0.9 -cons 60 -w 3

3) Uses an automatic method to decide optimal thresholds, based in the gap percentage count over the whole alignment.

   trimal -in <inputfile> -out <outputfile> -gappyout

4) Uses an heuristic method to decide which is the best automated method to trim the input alignment.

   trimal -in <inputfile> -out <outputfile> -automated1

5) Removes a set of columns as indicated by the user. Note that the numbering of the columns start by 0.

   trimal -in <inputfile> -out <outputfile> -select { 0-7,12,15,23-40 }

6) Removes spurious sequences from the input alignment.

   trimal -in <inputfile> -out <outputfile> -resoverlap 0.75 -seqoverlap 80

7) Gets the trimAl's trimming summary in an HTML file.

   trimal -in <inputfile> -out <outputfile> -htmlout <htmlfile> -strict 

8) Gets the relationship between the columns from the output and input alignments.

   trimal -in <inputfile> -out <outputfile> -strictplus -colnumbering

9) Selects the most consistency alignment among a set of them. Note that the alignments should have the same sequences in the same order.

   trimal -compareset <pathfile> -out <outputfile>

10) Selects the most consistency alignment among a set of them. After that, applies some manual thresholds to the selected alignment.

   trimal -compareset <pathfile> -out <outputfile> -gt 0.8 -st 0.7 -ct 0.3

To compute a similarity score for protein alignments, trimAl uses the Blosum62 Similarity Matrix meanwhile for DNA or RNA alignments, trimAl uses the Identity Similarity Matrix by default. However, in any case the user can use any other matrix.

It is impossible to use all the trimAl's options at the same time. The first incompatibility is between -in (designed to work with a single file) and -compareset (designed to work with a set of files). Other incompatibility is between the statistical information options and the trimming methods; in order to use combination between those methods is necessary that an output file is defined. Other compatibility is between the output and html file, they should be different in order to avoid problem in their creation. It is important that a trimming is used when one or more among the options -colnumbering, -complementary and -htmlout is used.