alignment-thin1

Usage

Overview

Remove sequences or columns from an alignment.

General options:

Sequence filtering options:

-p arg, –protect arg

Sequences that cannot be removed (comma-separated).

-k arg, –keep arg

Remove sequences not in comma-separated list arg.

-r arg, –remove arg

Remove sequences in comma-separated list arg.

-l arg, –longer-than arg

Remove sequences not longer than arg.

-s arg, –shorter-than arg

Remove sequences not shorter than arg.

-c arg, –cutoff arg

Remove similar sequences with #mismatches < cutoff.

-d arg, –down-to arg

Remove similar sequences down to arg sequences.

–remove-gappy arg

Remove arg outlier sequences – defined as sequences that are missing too many conserved sites.

–conserved arg (=0.75)

Fraction of sequences that must contain a letter for it to be considered conserved.

Column filtering options:

Output options:

Examples:

Remove columns without a minimum number of letters:

% alignment-thin --min-letters=5 file.fasta > file-thinned.fasta

Remove sequences by name:

% alignment-thin --remove=seq1,seq2 file.fasta > file2.fasta

% alignment-thin --keep=seq1,seq2   file.fasta > file2.fasta

Remove short sequences:

% alignment-thin --longer-than=250 file.fasta > file-long.fasta

Remove similar sequences with <= 5 differences from the closest other sequence:

% alignment-thin --cutoff=5 file.fasta > more-than-5-differences.fasta

Remove similar sequences until we have the right number of sequences:

% alignment-thin --down-to=30 file.fasta > file-30taxa.fasta

Remove dissimilar sequences that are missing conserved columns:

% alignment-thin --remove-gappy=10 file.fasta > file2.fasta

Protect some sequences from being removed:

% alignment-thin --down-to=30 file.fasta --protect=seq1,seq2 > file2.fasta

% alignment-thin --down-to=30 file.fasta --protect=@filename > file2.fasta

Reporting bugs:

BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\c .

Please send bug reports to ⟨[email protected]⟩\c .