pxseqgen1

Sequence simulator under the gtr model

Usage

pxseqgen [OPTIONS] ...

Overview

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.

Releases

3 releases since Debian 10 (Buster); the text changed 2 times.

--citation since Debian 12 (Bookworm); -C since Debian 12 (Bookworm).