This repository contains python/processing scripts to help to visualize alignments for phylogenetics.
With this scripts you will be able to investigate your alignments for completeness. It is still in a very early development stage, so beware of bugs and problems.
calc_miss.py takes a non-truncated FASTA alignment as input and calculates the relative completeness (number of available nucleotides relative to the number of taxa) per nucleotide position. This can then be used in viz_aln.pde, which will create a plot showing the acquired values for each alignment position.
- MacOS X or other Unix like operating system (Windows Version in the works)
- python 2.7.8+, which comes with most Unix like systems
- Processing2
Create your completeness data:
./calc_miss.py your_alignment.fas > out.txt
Visualize alignment:
Execute align_viz.pde in Processing, if you have multiple loci, ajust to locus boundaries in your alignment.
Alignment visualization and the corresponding scripts have first been used in this paper:
Philipp Resl, Kevin Schneider, Martin Westberg, Christian Printzen, Zdeněk Palice, Göran Thor, Alan Fryday, Helmut Mayrhofer and Toby Spribille (2015) Diagnostics for a troubled backbone: testing topological hypotheses of trapelioid lichenized fungi in a large-scale phylogeny of Ostropomycetidae (Lecanoromycetes). Fungal Diversity (in press)
Copyright (C) 2014 Philipp Resl
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program in the file LICENSE. If not, see http://www.gnu.org/licenses/.