p3-submit-gene-tree¶
Submit a Gene Phylogeny Tree Request¶
This script submits a request to build a phylogenetic tree of protein sequences. It accepts as input a group of FASTA files, and forms them into a tree using various criteria and methods.
Usage Synopsis¶
p3-submit-gene-tree [options] output-path output-name
Start a gene phylogeny job, producing output in the specified workspace path, using the specified name for the base filename of the output files.
Command-Line Options¶
–workspace-path-prefix
Base workspace directory for relative workspace paths.
–workspace-upload-path
Name of workspace directory to which local files should be uplaoded.
–overwrite
If a file to be uploaded already exists and this parameter is specified, it will be overwritten; otherwise, the script will error out.
–sequences
Main list of FASTA input files. These can be protein fasta files or DNA fasta files. For multiple files, specify the option multiple times.
–trim-threshold
Alignment end-trimming threshold.
–gap-threshold
Threshold for deleting alignments with large gaps.
–dna
If specified, the inputs are assumed to be DNA sequences. The default is protein sequences.
–substitution-model
Substitution model to use. The options are
HKY85
,JC69
,K80
,F81
,F84
,TN93
,GTR
,LG
,WAG
,JTT
,MtREV
,Dayhoff
,DCMut
,RtREV
,CpREV
,VT
,AB
,Blosum62
,MtMam
,MtArt
,HIVw
, orHIVb
.
–recipe
Recipe for building the tree. The options are
RAxML
,PhyML
, orFastTree
. The default isRAxML
.
The following options are used for assistance and debugging.
–help
Display the command-line usage and exit.
–dry-run
Display the JSON submission string and exit without invoking the service or uploading files.