pxrecode1

Usage

Overview

Nucleotide sequence recoding. This will take fasta, fastq, phylip, and nexus formats from a file or STDIN.

Options

-s, --seqf=FILE

input sequence file, STDIN otherwise

-r, --recode=STRING

string identifying recoding scheme (default: RY)

Supported recodings (use any valid combination):

R = A|G Y = C|T S = C|G W = A|T M = A|C K = G|T B = C|G|T D = A|G|T H = A|C|T V = A|C|G

-o, --outf=FILE

output sequence 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.