pxlssq1

Usage

Overview

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.