Man page - pxseqgen(1)
Packages contas this manual
- pxtscale(1)
- pxs2fa(1)
- pxrecode(1)
- pxlstr(1)
- pxssort(1)
- pxrevcomp(1)
- pxrms(1)
- pxvcf2fa(1)
- pxmono(1)
- pxtrt(1)
- pxt2new(1)
- pxcolt(1)
- pxconsq(1)
- pxlog(1)
- pxrmt(1)
- pxboot(1)
- pxupgma(1)
- pxs2nex(1)
- pxfqfilt(1)
- pxtcomb(1)
- pxrlt(1)
- pxrr(1)
- pxmrcacut(1)
- pxmrca(1)
- pxrls(1)
- pxtcol(1)
- pxsstat(1)
- pxclsq(1)
- pxbdfit(1)
- pxmrcaname(1)
- pxnj(1)
- pxcltr(1)
- pxs2phy(1)
- pxcontrates(1)
- pxtlate(1)
- pxt2nex(1)
- pxbdsim(1)
- pxcomp(1)
- pxbp(1)
- pxpoly(1)
- pxstrec(1)
- pxnw(1)
- pxcat(1)
- pxsw(1)
- pxrmk(1)
- pxseqgen(1)
- pxtgen(1)
- pxlssq(1)
- pxaa2cdn(1)
Package: phyx
apt-get install phyx
apt-get install phyx
Manuals in package:
Documentations in package:
Manual
| PXSEQGEN(1) | User Commands | PXSEQGEN(1) |
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
| June 2024 | pxseqgen 1.3.1 |