Provided by: phyx_1.0+ds-1_amd64
NAME
pxseqgen - Basic sequence simulator under the GTR model.
SYNOPSIS
pxseqgen [OPTION]...
DESCRIPTION
Basic sequence simulator under the GTR model. This will take fasta, fastq, phylip, and nexus inputs. -t, --treef=FILE input treefile, stdin otherwise -o, --outf=FILE output seq file, stout 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) -h, --help display this help and exit -V, --version display version and exit
REPORTING BUGS
Report bugs to: <https://github.com/FePhyFoFum/phyx/issues> phyx home page: <https://github.com/FePhyFoFum/phyx>
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.