Trimming Methods

Meta Automated Methods

Meta Automated methods analyze your alignment to decide between automated statistical methods.
Currently, only Automated1 is available, and it will analyze your MSA and select between Strict and Gappyout

Method	Description	Example of use
Automated1	Chooses between Strict and Gappyout Optimized for Maximum Likelihood phylogenetic tree reconstruction	bin/trimal -in dataset/example.007.AA.fasta -automated1

Automated Statistical Methods

Automated Statistical methods will search for optimum statistic thresholds to clean your alignment using statistics distribution.

Method	Description	Example of use
Strict	Uses Gaps and Similarity statistics to clean the alignment.	bin/trimal -in dataset/example.007.AA.fasta -strict
Strictplus	Uses Gaps and Similarity statistics to clean the alignment. Optimized for Neighbour Joining phylogenetic tree reconstruction	bin/trimal -in dataset/example.007.AA.fasta -strictplus
Gappyout	Uses Gaps statistic to clean the alignment.	bin/trimal -in dataset/example.007.AA.fasta -gappyout

Manual Threshold Methods

Manual Threshold methods allow the user to provide thresholds and windows for each statistic available.
It also allows the user to obtain the raw values for each statistic, per column and accumulative.

Statistic Name	Threshold Argument	Window Argument	Statistic Per Colum Argument	Statistic Accumulative Argument	Example of use
Gaps	-gt <n> [0 - 1]	-gw <n> [0 - 1/4*N]	-sgc	-sgt	bin/trimal -in dataset/example.007.AA.fasta -gt 0.5 -gw 2
Similarity	-st <n> [0 - 1]	-sw <n> [0 - 1/4*N]	-ssc	-sst	bin/trimal -in dataset/example.007.AA.fasta -st 0.5 -sw 2
Consistency	-ct <n> [0 - 1]	-cw <n> [0 - 1/4*N]	-sfc	-sft	bin/trimal -compareset data -ct 0.5 -cw 2

N = Number of residues in the input alignment

Manual Overlap Threshold Methods

Manual overlap allows to remove sequences based on two values: Sequence Overlap and Residue Overlap.

Sequence overlap indicates the minimum percentage of kept residues to keep a sequence.
Residue overlap indicates the minimum percentage of overlap (same residue on same position on the rest of sequences) to keep a residue.

Overlap Level	Command line argument
Sequence	-seqoverlap <n> [0-100]
Residue	-resoverlap <n> [0-1]

Manual Methods

Manual methods allow the user to provide a pattern to remove residues or sequences.

Method	Command line argument	Example of use
Sequences	-selectseqs { pattern }	bin/trimal -in dataset/example.007.AA.fasta -selectseqs { 0,4 }
Residues	-selectcols { pattern }	bin/trimal -in dataset/example.007.AA.fasta -selectcols { 1-4 }

The user must provide a pattern after the argument.
This pattern is a set of comma separated values:

 
 bin/trimal -in dataset/example.010.AA.fasta -selectseqs { 0,1,2 }

This would delete sequences 0, 1, and 2

Instead of providing raw position IDs, the user can also provide ranges, by separating start and end with a hyphen:

 
 bin/trimal -in dataset/example.010.AA.fasta -selectseqs { 0-2 }

This would delete sequences 0, 1, and 2

Combination of both separators are allowed:

 
 bin/trimal -in dataset/example.010.AA.fasta -selectcols { 0,4-6,12,16-18 }

This would delete sequences 0, 4, 5, 6, 12, 16, 17 and 18

Meaning the call above is synonymous to the following:

 
 bin/trimal -in dataset/example.010.AA.fasta -selectcols { 0,4,5,6,12,16,17,18 }

This would delete columns 0, 4, 5, 6, 12, 16, 17 and 18

    Combination of both are also allowed:

Automated Methods

Automated methods will remove columns based on raw gaps values.

Method	Description	Example of use
NoGaps	Removes any column containing at least, one gap	bin/trimal -in dataset/example.007.AA.fasta -nogaps
NoAllGaps	Removes columns containing only gaps	bin/trimal -in dataset/example.007.AA.fasta -noallgaps

Trimming Tweaks

Custom Matrix

Similarity values are obtained using a reference matrix
While trimAl contains matrices for each sequence type, the user can provide their own matrices.

Examples of these matrices can be found on the dataset folder:

matrix.BLOSUM62

a R N D C Q E G H I L k M F P S T W Y V
A +4 -1 -2 -2 +0 -1 -1 +0 -2 -1 -1 -1 -1 -2 -1 +1 +0 -3 -2 +0
R -1 +5 +0 -2 -3 +1 +0 -2 +0 -3 -2 +2 -1 -3 -2 -1 -1 -3 -2 -3
N -2 +0 +6 +1 -3 +0 +0 +0 +1 -3 -3 +0 -2 -3 -2 +1 +0 -4 -2 -3
D -2 -2 +1 +6 -3 +0 +2 -1 -1 -3 -4 -1 -3 -3 -1 +0 -1 -4 -3 -3
C +0 -3 -3 -3 +9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1
Q -1 +1 +0 +0 -3 +5 +2 -2 +0 -3 -2 +1 +0 -3 -1 +0 -1 -2 -1 -2
E -1 +0 +0 +2 -4 +2 +5 -2 +0 -3 -3 +1 -2 -3 -1 +0 -1 -3 -2 -2
G +0 -2 +0 -1 -3 -2 -2 +6 -2 -4 -4 -2 -3 -3 -2 +0 -2 -2 -3 -3
H -2 +0 +1 -1 -3 +0 +0 -2 +8 -3 -3 -1 -2 -1 -2 -1 -2 -2 +2 -3
I -1 -3 -3 -3 -1 -3 -3 -4 -3 +4 +2 -3 +1 +0 -3 -2 -1 -3 -1 +3
L -1 -2 -3 -4 -1 -2 -3 -4 -3 +2 +4 -2 +2 +0 -3 -2 -1 -2 -1 +1
K -1 +2 +0 -1 -3 +1 +1 -2 -1 -3 -2 +5 -1 -3 -1 +0 -1 -3 -2 -2
M -1 -1 -2 -3 -1 +0 -2 -3 -2 +1 +2 -1 +5 +0 -2 -1 -1 -1 -1 +1
F -2 -3 -3 -3 -2 -3 -3 -3 -1 +0 +0 -3 +0 +6 -4 -2 -2 +1 +3 -1
P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 +7 -1 -1 -4 -3 -2
S +1 -1 +1 +0 -1 +0 +0 +0 -1 -2 -2 +0 -1 -2 -1 +4 +1 -3 -2 -2
T +0 -1 +0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 +1 +5 -2 -2 +0
W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 +1 -4 -3 -2 +1 +2 -3
Y -2 -2 -2 -3 -2 -1 -2 -3 +2 -1 -1 -2 -1 +3 -3 -2 -2 +2 +7 -1
V +0 -3 -3 -3 -1 -2 -2 -3 -3 +3 +1 -2 +1 -1 -2 -2 +0 -3 -1 +4

matrix.Degenerated_DNA

A C D G K M S R T W Y
A 1 0 0 0 0 0 0 0 0 0 0
C 0 1 0 0 0 0 0 0 0 0 0
D 0 0 1 0 0 0 0 0 0 0 0
G 0 0 0 1 0 0 0 0 0 0 0
K 0 0 0 0 1 0 0 0 0 0 0
M 0 0 0 0 0 1 0 0 0 0 0
S 0 0 0 0 0 0 1 0 0 0 0
R 0 0 0 0 0 0 0 1 0 0 0
T 0 0 0 0 0 0 0 0 1 0 0
W 0 0 0 0 0 0 0 0 0 1 0
Y 0 0 0 0 0 0 0 0 0 0 1

Complementary

To extend the capability of trimAl, it is possible to obtain the complementary alignment.
This means, flipping the values of residues to keep/reject.

Terminal Only

Terminal Only option allows you to only trim the alignment outside the central block.
Central Block is defined as the block which contains
the center of the alignments and doesn't contain any gap inside.
Considering the Central Block as the best alignment section of an alignment,
due to be the one being built with no gaps,
we can trim the alignment keeping this Central Block untouched.

Block

Block argument allows to clean the alignment using different methods,
and later keep only residues that fall inside a keep-residues block of
the specified number of residues.
This allows us to remove columns that obtained good scores by random chance.

Clusters

It is possible to apply a clusterization of the sequences,
to keep only the most representative sequences of the variability
of the whole alignment.

It will output a alignment with the most representative sequence
for each cluster.

The user must provide the number of clusters to create, which is the
same as the number of sequences present on the final alignment;

Max Identity

Max Identity allows us to remove sequences with an identity
bigger than a user-provided threshold.

This removes the sequences that are too similar.

Compareset

Compareset allows the user to provide multipe MSA and to obtain Consistency scores.
These scores can be used to select the most consistent alignment in the set provided
or to use them as a trimming statistics to remove columns that are not consistent enough
among the set.

While Compareset will select the most consistent alignment, it is possible to force it to
select an specific alignment by using the -forceselect argument.

When an output file is provided, a summary of the compareset results is provided.

> cat alignments_comparison

dataset/example.010.a.AA.fasta
dataset/example.010.b.AA.fasta
dataset/example.010.c.AA.fasta

Summary chart

File:           dataset/example.010.a.AA.fasta
Values:         Sequences: 8    Residues: 187   Pond. Hits:  133.881    %Consistency: 0.715941

File:           dataset/example.010.b.AA.fasta
Values:         Sequences: 8    Residues: 188   Pond. Hits:   120.27    %Consistency: 0.639735

File:           dataset/example.010.c.AA.fasta
Values:         Sequences: 8    Residues: 188   Pond. Hits:  122.744    %Consistency: 0.652893
                                        --------------

File Selected:  dataset/example.010.a.AA.fasta
Value:          0.715941

Minimum Alignment Conservation Threshold

It is possible, depending on the MSA provided and the trimming methods selected
to trim the MSA in a excessively aggresive way.

This may lead to a MSA with few or no residues.

To solve this issue, one of the solutions proposed is to conserve
a minimum percentage of the alignment.

To do so, the alignment will start on the center of the alignment,
which is supposed to be better aligned than the terminal ends, and
starts recovering residues in both directions until the desired
Minimum Alignment Conservation Threshold has been achieved.

Other Tweaks

Column Numbering

Outputs the relationship between residues in the output and input alignment.
It will output a -1 if the residue was removed, and the original residue position otherwise.

  #ColumnsMap	-1, -1, -1, -1, -1, -1, 6, 7, 8, 9, 10, 11, 12, 13, -1, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, -1, -1, -1, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, -1, -1, -1, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, -1, -1, -1, -1, -1, -1, -1, -1, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, -1, -1, -1, -1, -1, -1, -1