pxseqgen - manual page for pxseqgen 1.3
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)
Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
phyx home page: <https://github.com/FePhyFoFum/phyx>
Copyright © 2015-2021 FePhyFoFum License GPLv3