Man page - pxseqgen(1)
Packages contains this manual
- pxs2fa(1)
- pxcomp(1)
- pxtcomb(1)
- pxsw(1)
- pxmono(1)
- pxlssq(1)
- pxssort(1)
- pxrmt(1)
- pxaa2cdn(1)
- pxpoly(1)
- pxcontrates(1)
- pxcat(1)
- pxs2phy(1)
- pxstrec(1)
- pxtgen(1)
- pxtcol(1)
- pxrecode(1)
- pxupgma(1)
- pxmrcaname(1)
- pxlstr(1)
- pxrevcomp(1)
- pxrr(1)
- pxtrt(1)
- pxrlt(1)
- pxbdfit(1)
- pxnw(1)
- pxbdsim(1)
- pxrmk(1)
- pxclsq(1)
- pxt2new(1)
- pxtlate(1)
- pxvcf2fa(1)
- pxrms(1)
- pxfqfilt(1)
- pxt2nex(1)
- pxcltr(1)
- pxlog(1)
- pxmrca(1)
- pxseqgen(1)
- pxbp(1)
- pxnj(1)
- pxsstat(1)
- pxtscale(1)
- pxconsq(1)
- pxs2nex(1)
- pxrls(1)
- pxmrcacut(1)
- pxcolt(1)
- pxboot(1)
apt-get install phyx
Manual
PXSEQGEN
NAMESYNOPSIS
DESCRIPTION
OPTIONS
CITATION
AUTHOR
REPORTING BUGS
COPYRIGHT
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