NAME

       pxseqgen - sequence simulator under the GTR model

SYNOPSIS

       pxseqgen [OPTIONS]...

DESCRIPTION

       Basic  sequence  simulator  under the GTR model.  This will take fasta, fastq, phylip, and
       nexus formats from a file or STDIN.

OPTIONS

       -t, --treef=FILE
              input treefile, STDIN otherwise

       -l, --length=INT
              length of sequences to generate. default is 1000

       -b, --basef=Input
              comma-delimited base freqs in order: A,C,G,T. default is equal

       -g, --gamma=INT
              gamma shape value. default is no rate variation

       -i, --pinvar=FLOAT
              proportion of invariable sites. default is 0.0

       -r, --ratemat=Input
              comma-delimited  input  values  for   rate   matrix.   default   is   JC69   order:
              A<->C,A<->G,A<->T,C<->G,C<->T,G<->T

       -w, --aaratemat=Input
              comma-delimited  amino  acid  rate  matrix.  default  is  all  freqs equal order is
              ARNDCQEGHILKMFPSTWYV

       -q, --aabasefreq=Input AA frequencies, order: ARNDCQEGHILKMFPSTWYV

       -c, --protein
              run as amino acid

       -n, --nreps=INT
              number of replicates

       -x, --seed=INT
              random number seed, clock otherwise

       -a, --ancestors
              print the ancestral node sequences. default is no use -p for the nodes labels

       -p, --printnodelabels
              print newick with internal node labels. default is no

       -m, --multimodel=Input specify multiple models across tree
              input is as follows:

       A<->C,A<->G,A<->T,C<->G,C<->T,G<->T,Node#,A<->C,A<->G,A<->T,C<->G,C<->T,G<->T
              EX:.3,.3,.3,.3,.3,1,.3,.3,.2,.5,.4

       -k, --rootseq=STRING
              set root sequence. default is random (from basefreqs)

       -o, --outf=FILE
              output seq 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 © 2015-2024 FePhyFoFum License GPLv3