NAME¶

pxseqgen - manual page for pxseqgen 1.3

SYNOPSIS¶

pxseqgen [OPTIONS]...

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

-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

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.

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

July 2021

pxseqgen 1.3