pxclsq1

Usage

Overview

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.

Options

-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

Citation

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.