table of contents
PXSEQGEN(1) | User Commands | PXSEQGEN(1) |
NAME¶
pxseqgen - manual page for pxseqgen 1.3
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 © 2015-2021 FePhyFoFum License GPLv3
July 2021 | pxseqgen 1.3 |