P-GnomeX_v3.2.2 20071204
Phylogenomenclature OS X Installation instructions:
NOTE BENE: We suggest that you run P-Gnome on OS X 10.4 or 10.5; however, there have been no OS specific problems with running the application on 10.1+.
Stuffit is required for the downloads contained on this page. Generally this is already installed on your OSX system.
1. Download the appropriate package:
==> If you do not have BLAST installed (or are not sure*) [click here -- pgnomeXfull.mpkg.tgz ~35.9M].
* it is recommended that you consult your systems administrator to determine if you have BLAST installed or not.
==> If you already have BLAST installed [click here -- pgnomeX.pkg.tgz ~180k].
==> If you would like to download sample input files [click here -- pgnome_examples.tgz ~ 4k].
testSeqsTre.nex -- this is an example NON-INTERLEAVED MacClade File, containing both a matrix and a SINGLE tree
testSeqs.txt -- this is a test set file, in FASTA format (the seqs are the same as the input)
2. Uncompress the zip file.
After you have downloaded the package -- if your browser has not already uncompressed the file -- double-click it, and this should automatically uncompress the package (.pkg or .mpkg file).
3. Double click the package file.
This will install P-Gnome and P-Elf, the scripts for Phylogenomenclature.
Interactive-mode for either P-Gnome or P-Elf is executable by simply typing (at the terminal command line):
P-Gnome
or
P-Elf
In order to create a rule set for analysis and subsequent classification, you need to run P-Gnome
Command-line syntax for P-Gnome is as follows:
P-Gnome [MacClade File] [output directory] [Do Compound Analysis]
Where,
[MacClade File] -- is the name of the MacClade file that contains the matrix and tree
[output directory] -- is the name of the directory to save the rules into
[Do Compound Analysis] -- setting for whether to search for compounds or not; 1 = no, 2 = yes
Example run:
P-Gnome testSeqsTre.nex output 1
In order to now classify sequences contained in a fasta file, you need to run P-Elf.
Command-line syntax for P-Elf is as follows:
P-Elf -ruleDir=[ruleDir] -input=[fastaFile] -out=[mac|txt]
Where,
[ruleDir] -- is the name of the [output directory] from P-Gnome that you wish to use.
[fastaFile] -- is the name of the file that contains the query sequences in fasta format
[mac|txt] -- (optional) is the output format to the stdout. "mac" will output macClade format. "txt" will be a plain text listing. (mac is default)
Information on the files created by P-Gnome:
All the outputted files are stored in the directory that you name. They contain the following types of files: