Sequence Removal

Based on a list of IDs, you can remove sequences in a collection of alignments. This feature is the opposite of segul extract feature. It is faster than segul extract if you remove less than a half of the sequences.

Remove sequences based on a list of IDs

You can remove sequences based on a list of sequence IDs. Input a list of IDs as a string separated by semi-colons.

segul sequence remove --dir [alignment-dir] -f [sequence-format-keyword] --id="[list-of-id]"

Example:

segul sequence remove --dir ./data/ -f fasta --id="seq_1;seq_2;seq_3"

warning

The equal sign "=" and quotation marks " are required to input a list of IDs.

Remove sequences based on a regular expression

Using regular expression:

segul sequence remove --dir [alignment-dir] -f [sequence-format-keyword] --re=["regex"]

Example:

Command below will remove all sequences whose IDs with the name started with Homo.

segul sequence remove --dir ./data/ -f fasta --re="^Homo"