This is the Linux app named Pontos whose latest release can be downloaded as Pontos-3.0-src.zip. It can be run online in the free hosting provider OnWorks for workstations.
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Pontos
DESCRIPTION
Pontos is an easy-to-use, graphical Java program for the calculation of uncorrected distance (or similarity) matrices from DNA sequence alignments in PHYLIP format. It also creates "difference" alignments from regular ones (and vice-versa).
It can handle gaps and ambiguities in different ways.
Gaps can be:
- all used;
- all ignored;
- ignored only at the ends of the sequences, in a pairwise manner;
- ignored only at the ends, but now globally (in effect trimming the whole alignment to the farthest sequences from the ends).
Ambiguities (things like R, Y, N, W, etc. in a DNA sequence) can be treated like:
- consider ambiguities as always different;
- consider ambiguity as partially different (e.g. R would be 0.5 different from A or G);
- ignore ambiguities in each pairwise comparison;
- remove all columns, globally, that show any ambiguity.
Pontos was written in Linux, but should run in any system where Java works. Pontos is licensed under the GPL version 3.
Audience
Science/Research, End Users/Desktop
User interface
Java Swing
Programming Language
Java
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/pontos/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
