R"(
[b][u]Some Examples:[r]

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

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

[b]2) As above but, the gap score is averaged over a window starting
   3 positions before and ending 3 positions after each column.

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

[b]3) Use an automatic method to decide optimal thresholds, based in the gap scores
   from input alignment. (see User Guide for details).

[r]   trimal -in <inputfile> -out <outputfile> -gappyout

[b]4) Use automatic methods to decide optimal thresholds, based on the combination
   of gap and similarity scores. (see User Guide for details).

[r]   trimal -in <inputfile> -out <outputfile> -strictplus

[b]5) Use an heuristic to decide the optimal method for trimming the alignment.
   (see User Guide for details).

[r]   trimal -in <inputfile> -out <outputfile> -automated1

[b]6) Use residues and sequences overlap thresholds to delete some sequences from the
   alignment. (see User Guide for details).

[r]   trimal -in <inputfile> -out <outputfile> -resoverlap 0.8 -seqoverlap 75

[b]7) Selection of columns to be deleted from the alignment. The selection can
   be a column number or a column number interval. Start from 0

[r]   trimal -in <inputfile> -out <outputfile> -selectcols { 0,2,3,10,45-60,68,70-78 }

[b]8) Get the complementary alignment from the alignment previously trimmed.

[r]   trimal -in <inputfile> -out <outputfile> -selectcols { 0,2,3,10,45-60,68,70-78 } -complementary

[b]9) Selection of sequences to be deleted from the alignment. Start from 0

[r]   trimal -in <inputfile> -out <outputfile> -selectseqs { 2,4,8-12 }

[b]10) Select the 5 most representative sequences from the alignment

[r]   trimal -in <inputfile> -out <outputfile> -clusters 5
)"