Pontos Icon


Pontos calculates distance matrices from DNA sequence alignments.

Add a Review
1 Download (This Week)
Last Update:
Download Pontos-3.0.jar
Browse All Files



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.

Pontos Web Site


Write a Review

User Reviews

Be the first to post a review of Pontos!

Additional Project Details

Intended Audience

Science/Research, End Users/Desktop

User Interface

Java Swing

Programming Language




Thanks for helping keep SourceForge clean.

Screenshot instructions:
Red Hat Linux   Ubuntu

Click URL instructions:
Right-click on ad, choose "Copy Link", then paste here →
(This may not be possible with some types of ads)

More information about our ad policies

Briefly describe the problem (required):

Upload screenshot of ad (required):
Select a file, or drag & drop file here.

Please provide the ad click URL, if possible:

Get latest updates about Open Source Projects, Conferences and News.

Sign up for the SourceForge newsletter:

No, thanks