pxtlate - translate DNA alignment to amino acids

Author

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

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.

Copyright

       Copyright © 2015-2024 FePhyFoFum License GPLv3

pxtlate 1.3.1                                       June 2024                                         PXTLATE(1)

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.

Name

       pxtlate - translate DNA alignment to amino acids

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

Reporting Bugs

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