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, or HIVb.

  • –recipe

Recipe for building the tree. The options are RAxML, PhyML, or FastTree. The default is RAxML.

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.