I encourage everyone to have a look at a new PIA implementation that is available at: https://github.com/AlenaKizenko/pia3_amphipod_opsins
Drozdova et al. (2021) have done a great job at packaging PIA and simplifying the installation via conda (among many other improvements).
Drozdova, P., Kizenko, A., Saranchina, A. et al. The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae). BMC Ecol Evo 21, 81 (2021). https://doi.org/10.1186/s12862-021-01806-9
This collection of scripts is written in bash, perl, and python.
Make sure dependencies are installed and configured before running. Dependencies include: BLAST, MAFFT, R (w/ ape and phytools packages), Perl, BioPerl, NumPy, SciPy, statsmodels (for python), Java, RAxML, USEARCH, … and any dependencies these might have.
Special thanks to Dr. Todd Oakley's lab at UCSB for the original galaxy scripts on which we have based this pipeline. Original versions can be found at: https://bitbucket.org/osiris_phylogenetics/osiris_phylogenetics and https://bitbucket.org/osiris_phylogenetics/pia
Jorge L. Perez-Moreno, Danielle DeLeo, Heather D. Bracken-Grissom CRUSTOMICS Lab at Florida International University 04/05/2017
- Edit pia.pl :
- Line 1: This should reflect the actual path to your perl installation
- Line 15: Path to your PIA folder
- Line 18: Path to your LIT folder, usually within PIA’s unless you want it elsewhere
- Line 94: You might want to change -num_threads to the number of CPU threads you want to allocate to BLAST
- Lines 714 & 715: This should reflect the raxml version you’re using. The -T again is changeable to allocate CPU threads, and -m corresponds to the model of evolution for RAxML to use if customization is required.
- Line 721: Modify path to PIA & phyutility
- Edit pia/phyutility/phyutility
- Change Path to reflect your installation
- Edit pia/phylographics/tab2trees.sh
- Change Paths in lines 3 & 15
PIA (Phylogenetically Informed Annotation) is a set of tools for the Galaxy Bioinformatics Platform. In general, PIA uses BLAST, an alignment program, and RAxML's read placement algorithm to put unknown sequences into pre-calculated phylogenetic trees. We provide 102 genes called LIT (Light Interaction Toolkit) - vision genes like phototransduction genets - for use in PIA.
License: All original source code for PIA is available under the MIT license (http://opensource.org/licenses/mit-license.html). See below: The MIT License (MIT) Copyright (c) 2014 Speiser et al
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.