NAME¶

pxtlate - translate DNA alignment to amino acids

SYNOPSIS¶

pxtlate [OPTIONS]...

DESCRIPTION¶

Translate DNA alignment to amino acids. This will take fasta, fastq, phylip, and nexus formats from a file or STDIN. NOTE: assumes sequences are in frame.

OPTIONS¶

-s, --seqf=FILE

input nucleotide sequence file, STDIN otherwise

-t, --table=STRING

which translation table to use. currently available: 'std' (standard, default) 'vmt' (vertebrate mtDNA) 'ivmt' (invertebrate mtDNA) 'ymt' (yeast mtDNA)

-o, --outf=FILE

output aa 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.

AUTHOR¶

Written by Joseph F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim)

REPORTING BUGS¶

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

COPYRIGHT¶

Copyright © 2015-2021 FePhyFoFum License GPLv3