alignment-thin(1) | alignment-thin(1) |
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:¶
- --protect arg
- Sequences that cannot be removed (comma-separated).
- --remove arg
- Remove sequences in comma-separated list arg.
- --longer-than arg
- Remove sequences not longer than arg.
- --shorter-than arg
- Remove sequences not shorter than arg.
- --cutoff arg
- Remove similar sequences with #mismatches < cutoff.
- --down-to arg
- Remove similar sequences down to arg sequences.
- --remove-crazy 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:¶
- --min-letters arg
- Remove columns with fewer than arg letters.
- --remove-unique arg
- Remove insertions in a single sequence if longer than arg letters
OUTPUT OPTIONS:¶
- --sort
- Sort partially ordered columns to group similar gaps.
- --show-lengths
- Just print out sequence lengths.
- --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
Remove short sequences:
-
% alignment-thin --longer-than=250 file.fasta > file-long.fasta
Remove sequences with <= 5 differences from the closest other sequence:
-
% alignment-thin --cutoff=5 file.fasta > more-than-5-differences.fasta
Like --cutoff, but stop when 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-crazy=10 file.fasta > file2.fasta
Protect some sequences from being removed:
-
% alignment-thin --down-to=30 file.fasta --protect=seq1,seq2 > file2.fasta
REPORTING BUGS:¶
BAli-Phy online help: <http://www.bali-phy.org/docs.php>.Please send bug reports to <bali-phy-users@googlegroups.com>.
AUTHORS¶
Benjamin Redelings.Feb 2018 |