pxclsq - clean positions or taxa with too much ambiguous data
Clean alignments by removing positions/taxa with too much
ambiguous data. This will take fasta, fastq, phylip, and nexus formats from
a file or STDIN. Results are written in fasta format.
- -s,
--seqf=FILE
- input sequence file, STDIN otherwise
- -p,
--prop=DOUBLE
- proportion required to be present, default=0.5
- -e, --empty
- remove columns that are completely empty (- or ?)
- -m,
--min=INT
- the minimum number of good characters required per site - a min of 1 is
equivalent to -e above
- -t, --taxa
- consider missing data per taxon (default: per site)
- -c, --codon
- examine sequences by codon rather than site - requires all sequences be in
frame and of correct length
- -i, --info
- report counts of missing data and exit - combine with -t to get
report by taxon (rather than site) - combine with -c to use codons
as units
- -v, --verbose
- more verbose output (i.e. if entire seqs are removed)
- -o,
--outf=FILE
- output fasta file, STOUT otherwise
- -h, --help
- display this help and exit
- -V, --version
- display version and exit
- -C,
--citation
- display phyx citation and exit
Brown, Joseph W., Joseph F. Walker, and Stephen A. Smith. 2017.
Phyx: phylogenetic tools for unix. Bioinformatics 33(12): 1886-1888.
https://doi.org/10.1093/bioinformatics/btx063.
Written by Joseph F. Walker, Joseph W. Brown, Stephen A. Smith
(blackrim)
Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
phyx home page: <https://github.com/FePhyFoFum/phyx>
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