pxlssq(1)

NAME

pxlssq - print sequence file summary

SYNOPSIS

pxlssq [OPTIONS]...

DESCRIPTION

Print sequence file summary. By default returns all properties. Alternatively choose 1 property. This will take fasta, phylip, and nexus formats from a file or STDIN.

OPTIONS

-s, --seqf=FILE: input seq file, STDIN otherwise

-i, --indiv: output stats for individual sequences

-n, --nseq: return the number of sequences

-c, --nchar: return the number of characters (only if aligned) - for unaligned seqs, use with -i flag

-l, --labels: return all taxon labels (one per line)

-p, --prot: force interpret as protein (if inference fails)

-a, --aligned: return whether sequences are aligned (same length)

-f, --freqs: return character state frequencies

-m, --missing: return the proportion of missing (-,?) characters

-o, --outf=FILE: output stats 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.

AUTHOR

Written by Joseph F. Walker, Joseph W. Brown

REPORTING BUGS

Report bugs to: <https://github.com/FePhyFoFum/phyx/issues> phyx home page: <https://github.com/FePhyFoFum/phyx>