1.2.59 Trim alignments using TrimAl - run on XSEDE Salvador Capella-Gutierrez, Jose M. Silla-Martinez and Toni Gabaldon. Salvador Capella-Gutierrez, Jose M. Silla-Martinez and Toni Gabaldon. trimAl: a tool for automated alignment trimming (2009). Phylogeny / Alignment trimal_xsede trimal_comet perl "" 0 number_nodes 2 scheduler.conf perl "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=$select_numcores\\n" infile Input File perl "-in infile.txt" 99 infile.txt all_results * runtime 1 scheduler.conf Maximum Hours to Run (up to 168 hours) 0.5 The maximum hours to run must be less than 168 perl $runtime > 168.0 The maximum hours to run must be greater than 0.05 perl $runtime < 0.05 perl "runhours=$value\\n" Please adjust the number of cores only if your job ran out of memory perl $select_numcores > 1 The job will run on 1 processor as configured. If it runs for the entire configured time, it will consume 1 X $runtime cpu hours perl $select_numcores <= 1 The job will run on $select_numcores processor as configured. If it runs for the entire configured time, it will consume $select_numcores X $runtime cpu hours perl $select_numcores > 1 Estimate the maximum time your job will need to run. We recommend testimg initially with a < 0.5hr test run because Jobs set for 0.5 h or less dependably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. select_numcores How many cores? 1 The number of cores cannot exceed 8 perl $select_numcores > 8 Please adjust the number of cores only if your job ran out of memory perl $select_numcores > 1 select_complementary Get the complementary alignment (-complementary) perl ($value) ? "-complementary":"" complementary: This parameter lets the user get the complementary alignment, in other words, when the user uses this parameter trimAl will render the columns/sequences that would be deleted from the original alignment. select_colnumbering Get the relationship between the columns in the old and new alignment (-colnumbering) perl ($value) ? "-colnumbering":"" Sorry, colnumbering cant be used with statistical options perl $select_colnumbering && ($specify_noallgaps || $specify_gappyout || $specify_strict || $specify_strictplus || $specify_automated1 ) colnumbering: This parameter will provide you the relationship between the column numbers in the trimmed and the original alignment. similarity_matrixfile Specify a user-defined similarity matrix file perl (defined $value) ? "-matrix similarity_matrix.txt":"" similarity_matrix.txt window_params Manual Selection Parameters select_columns Selection of columns to be removed from the alignment. (-select) perl (defined $value) ? "-select { $value }":"" Sorry you cant mix manual and automatic analyses perl $select_columns && ($specify_noallgaps || $specify_nogaps || $specify_strict || $specify_strictplus || $specify_automated1 || $specify_gappyout ) This algorithm simply removes a set of columns as indicated by the user. The set of columns that will be removed has to be provided as individual column numbers separated by commas, and/or blocks of consecutive columns indicated as the first and last column number separated by hyphen. In the following example: select {n,l,m-k} where n and l are interpreted as single column numbers while m-k is a range of columns (from column m to column k, both included) to be deleted. Note that the numbering of the columns starts by 0. For instance, the command: select {2,7,20-25,80-100} will remove columns 2 and 7 and two blocks of columns ranging from column 20 to 25 and 80 to 100, respectively. specify_gapthreshold Fraction of sequences with a gap allowed (-gt) perl !defined $select_columns perl (defined $value) ? "-gt $value":"" Sorry the gap threshold is a percentage, and must be less tan or equal to one. perl defined $specify_gapthreshold && $specify_gapthreshold > 1 Sorry you cant mix manual and automatic analyses perl $select_columns && ($specify_noallgaps || $specify_nogaps || $specify_strict || $specify_strictplus || $specify_automated1 || $specify_gappyout ) After the selection of a gap score cutoff point, trimAl removes all of those columns that do not reach this value. In practice, this method basically detects the bimodal distribution of gap scores (gap rich and gap poor columns) in an alignment to subsequently get rid of the gap-rich mode. specify_similarity Minimum average similarity allowed (-st) perl !defined $select_columns perl (defined $value) ? "-st $value":"" Sorry the similarity threshold is a percentage, and must be less tan or equal to one. perl defined $specify_similarity && $specify_similarity > 1 Sorry you cant mix manual and automatic analyses perl $select_columns && ($specify_noallgaps || $specify_nogaps || $specify_strict || $specify_strictplus || $specify_automated1 || $specify_gappyout ) After the selection of a gap score cutoff point, trimAl removes all of those columns that do not reach this value. In practice, this method basically detects the bimodal distribution of gap scores (gap rich and gap poor columns) in an alignment to subsequently get rid of the gap-rich mode. specify_mincon Minimum percentage of the positions in the original alignment to conserve (-cons) perl !defined $select_columns perl (defined $value) ? "-cons $value":"" Sorry the conserved percentage must be greater than or equal to zero. perl defined $specify_mincon && $specify_mincon < 0 Sorry the percentage must be less than or equal to 100 perl defined $specify_mincon && $specify_mincon > 100 Sorry you cant mix manual and automatic analyses perl $select_columns && ($specify_noallgaps || $specify_nogaps || $specify_strict || $specify_strictplus || $specify_automated1 || $specify_gappyout ) The user can set up a conservation threshold which refers to the minimum percentage of columns from the input alignment that should be part of the trimmed alignment. This threshold is defined between 0 and 100. This threshold overrides all other thresholds. window_params Automatic Run Parameters specify_nogaps Remove all positions with gaps in the alignment (-nogaps) perl !defined $select_columns perl ($value) ? "-nogaps":"" Gap removal cant be used with manual removal of columns (-select) perl $specify_nogaps && $select_columns nogaps is equivalent to -gt 1; deletes all columns with at least one gap in it specify_noallgaps Remove columns composed only by gaps. (-noallgaps) perl !defined $select_columns perl ($value) ? "-noallgaps":"" Sorry you cant use -nogaps and -noallgaps together perl $specify_nogaps && $specify_noallgaps Sorry you cant select multiple automatic analyses perl $specify_noallgaps && ($specify_nogaps || $specify_strict || $specify_strictplus || $specify_automated1 || $specify_gappyout ) noallgaps removes those columns composed only by gaps specify_gappyout Use automated selection on "gappyout" mode (-gappyout) perl !defined $select_columns perl ($value) ? "-gappyout":"" Sorry you cant select multiple automatic analyses perl $specify_gappyout && ($specify_nogaps || $specify_strict || $specify_strictplus || $specify_automated1) Use automated selection on "gappyout" mode. This method only uses information based on gaps' distribution. (see User Guide). specify_strict Use automated selection on "strict" mode (-strict) perl !defined $select_columns perl ($value) ? "-strict":"" Sorry you cant select multiple automatic analyses perl $specify_strict && ($specify_nogaps || $specify_strictplus || $specify_automated1) Use automated selection on "strict" mode. This method combines a gappyout trimming with a subsequent trimming based on an automatically selected similarity threshold. (see User Guide). specify_strictplus Use automated selection on "strictplus" mode (-strictplus) perl !defined $select_columns perl ($value) ? "-strictplus":"" Sorry you cant select multiple automatic analyses perl $specify_strictplus &&($specify_nogaps || $specify_automated1) Use automated selection on "strictplus" mode. (Optimized for Neighbour Joining phylogenetic tree reconstruction). This method is similar to the -strict method, but they differ in that -strictplus automatically selects the block size for the final step of the algorithm. (see User Guide). specify_automated1 Use a heuristic selection of the automatic method based on similarity statistics. (-automated1) perl !defined $select_columns perl ($value) ? "-automated1":"" Use a heuristic selection of the automatic method based on similarity statistics. (see User Guide). (Optimized for Maximum Likelihood phylogenetic tree reconstruction). specify_resoverlap Minimum overlap of a positions with other positions in the column (-resoverlap) perl !defined $select_columns perl (defined $value) ? "-resoverlap $value":"" The overlap value should be between 0 and 1 perl $specify_resoverlap < 0 || $specify_resoverlap > 1 Please specify the sequence overlap value perl $specify_resoverlap && !defined $specify_seqoverlap Minimum overlap of a positions with other positions in the column to be considered a "good position". (see User Guide). The residue overlap threshold (-resoverlap) corresponds to the minimum residue overlap score for each residue specify_seqoverlap Minimum percentage of "good positions" that a sequence must have (-seqoverlap) perl !defined $select_columns perl (defined $value) ? "-seqoverlap $value":"" Please specify the residue overlap value perl $specify_seqoverlap && !defined $specify_resoverlap The sequence overlap threshold (-seqoverlap) sets up the minimum percentage of the residues for each sequence that should pass the residue overlap threshold in order to maintain the sequence in the new alignment. Sequences that do not pass the sequence overlap threshold will be removed from the alignment window_params Window Parameters specify_windowsize Window size, score of position i is the average of the window (i - n) to (i + n) (-w) perl !defined $select_columns perl (defined $value) ? "-w $value":"" This value establishes the number of columns at each side of a given position that trimAl has to consider when computing some scores, such as gap, conservation or consistency scores, for that position. When a window size is given, trimAl provides the average value of all columns considered specify_gapwindowsize Window size only applies to statistics/methods based on Gaps (-gw) perl !defined $select_columns perl (defined $value) ? "-gw $value":"" This value establishes the number of columns at each side of a given position that trimAl has to consider when computing some scores, gap for that position. When a window size is given, trimAl provides the average value of all columns considered specify_simwindowsize Window size only applies to statistics/methods based on Similarity (-sw) perl !defined $select_columns perl (defined $value) ? "-sw $value":"" This value establishes the number of columns at each side of a given position that trimAl has to consider when computing some scores, similarity for that position. When a window size is given, trimAl provides the average value of all columns considered specify_conwindowsize Window size only applies to statistics/methods based on Consistency (-cw) perl !defined $select_columns perl (defined $value) ? "-cw $value":"" This value establishes the number of columns at each side of a given position that trimAl has to consider when computing some scores, consistency for that position. When a window size is given, trimAl provides the average value of all columns considered output_params Output Parameters out_filename Specify the name of the output file perl ($value) ? "-out $out_filename":"" 4 out_htmlfilename Output file in html format perl ($value) ? "-htmlout $out_filename.html":"" 4 output_format Specify the output format Same as input -clustal Clustal -fasta Fasta -nbrf NBRF -nexus Nexus -mega Mega -phylip3.2 Phylip 3.2 -phylip Phylip perl $value 4 trimAl can change the output format for a given alignment. By default the output format is the same as the input one, but you can produce an output in different format with these options:. print_sgc Print gap percentage count for columns in the input alignment. (-sgc) perl ($value) ? "-sgc":"" print_sgt Print accumulated gap percentage count (-sgt) perl ($value) ? "-sgt":"" print_scc Print conservation values for columns in the input alignment (-scc) perl ($value) ? "-scc":"" print_sct Print accumulated conservation values count (-sct) perl ($value) ? "-sct":"" print_sident Print identity statistics for all sequences in the alignemnt. (-sident) perl ($value) ? "-sident":""