Alignment Trimming

Trim alignments based on the proportion of missing data or the number of parsimony informative sites. This feature will filter sites based on the specified parameters.

Note

This feature is available in SEGUL v0.23.0 and later versions. To check your SEGUL version, run in your terminal:

segul --version
# Compatible version example:
# segul 0.23.0

Check the Installation Guide to update SEGUL to the latest version.

Quick example

Assume we have an alignment file in FASTA format as follows:

>seq1
ATGCAT--A
>seq2
ATGCATA--
>seq3
ATGCAA-A-
>seq4
ATGCATA--

If we set the proportion of missing data to 0.5. It will generate an output without the last two sites using the following command:

segul align trim --dir alignments/ --missing-data 0.5

The output as follows. Note that the last two sites were removed because they had more than 50% missing data.

>seq1
ATGCAT-
>seq2
ATGCATA
>seq3
ATGCAA-
>seq4
ATGCATA

Detailed usage

Filtering based on the proportion of missing data

To trim alignments, use the align trim command with the following options:

segul align trim --dir <alignment-dir> --missing-data <value>

For example:

segul align trim --dir alignments/ --missing-data 0.5

Filtering based on parsimony informative sites

To trim based on the minimum threshold of parsimony informative sites, use the --pinf option:

segul align trim --dir <alignment-dir> --pinf <value>

For example, this command will retain sites with at least 50 parsimony informative sites:

segul align trim --dir alignments/ --pinf 50

Amino acid alignment trimming

If the input is amino acid sequences, you need to use the --datatype aa option. For example:

segul align trim --dir alignments/ --missing-data 0.5 --datatype aa

Specifying the output directory and format

By default, the output directory is Align-Trim. You can change the output directory name using the --output or -o option. For example, to name the output directory align-trim, use the command below:

segul align trim --dir alignments/ --output align-trim

To specify the output format, use the --output-format or -F option. The default output format is NEXUS. For example, to change the output format to FASTA, use the command below:

segul align trim --dir alignments/ --output-format fasta

All options

Option	Description
-d, --dir	Directory with alignments
-i, --input	Alignment files. Allows wildcards
-f, --input-format	Input format: auto (default), fasta, nexus, or phylip
--datatype	Data type: dna (default), aa, or ignore
--missing-data	Remove sites with a higher proportion of missing data
--pinf	Parsimony informative site threshold for keeping sites
-F, --output-format	Output format: nexus (default), phylip, fasta, nexus-int, phylip-int, or fasta-int
-o, --output	Output directory. Default: Align-Trim
--force	Overwrite an existing output directory
--log	Log file path. Default: segul.log