NAME
alignment-thin - Remove sequences or columns from an alignment.
SYNOPSIS
alignment-thin alignment-file [OPTIONS]
DESCRIPTION
Remove sequences or columns from an alignment.
GENERAL OPTIONS:
- -h, –help
-
Print usage information.
- -V, –verbose
-
Output more log messages on stderr.
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:
- -K arg, –keep-columns arg
-
Keep columns from this sequence
- -m arg, –min-letters arg
-
Remove columns with fewer than arg letters.
- -u arg, –remove-unique arg
-
Remove insertions in a single sequence if longer than arg letters
- -e, –erase-empty-columns
-
Remove columns with no characters (all gaps).
OUTPUT OPTIONS:
- -S, –sort
-
Sort partially ordered columns to group similar gaps.
- -L, –show-lengths
-
Just print out sequence lengths.
- -N, –show-names
-
Just print out sequence lengths.
- -F arg, –find-dups arg
-
For each sequence, find the closest other sequence.
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 .
AUTHORS
Benjamin Redelings.