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PAL: Phylogenetic Analysis Library

The PAL project is a collaborative effort to provide a high quality Java library for use in molecular evolution and phylogenetics. Updates of PAL are released in regular intervals. At present (version 1.4) PAL consists of approximately 200 public classes/interfaces … Continue reading

Rating: 5.0. From 1 vote.
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Posted in Genetics | Leave a comment

PHYLIP

PHYLIP Phylogeny Inference Package computer programs for inferring phylogenies Find PHYLIP at: http://evolution.genetics.washington.edu/phylip.html

Rating: 5.0. From 1 vote.
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Posted in Genetics | Leave a comment

PAML

Phylogenetic Analysis by Maximum Likelihood Find PAML at: http://abacus.gene.ucl.ac.uk/software/paml.html

Rating: 5.0. From 1 vote.
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Posted in Genetics | Leave a comment

HMMER

Profile hidden Markov models for biological sequence analysis. Find HMMER at: http://hmmer.janelia.org/

Rating: 4.7. From 10 votes.
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Posted in Bioinformatics | Leave a comment

Dynamite

Dynamite is a code generating language developed for sequence comparison methods. Find Dynamite at: http://www.sanger.ac.uk/Software/Dynamite/

Rating: 4.7. From 3 votes.
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Posted in Bioinformatics | Leave a comment

SwisTrack: Multi-Object Video Tracking Software

SwisTrack allows for tracking multiple objects such as insects or robots from a video stream provided by a file or directly from a camera. SwisTrack’s user interface allows adjusting parameters on the flight, and thus allow to find an optimal … Continue reading

Rating: 4.4. From 29 votes.
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Posted in Engineering, Life Sciences | Leave a comment

Phylogen

Phylogen implements some straight-forward birth-death models for simulating phylogenies. It is intended to be fast and flexible and can simulate very large trees (depending on memory and speed of computer). It will then optionally reconstruct trees only containing extant lineages … Continue reading

Rating: 4.4. From 8 votes.
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Posted in Evolution and Population Genetics | Leave a comment

BioJava

Java tools for processing biological data Find BioJava at: http://www.biojava.org/

Rating: 4.3. From 27 votes.
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Posted in Life Sciences | Leave a comment

ODIN

ODIN – Object Oriented Development Interface for NMR is a framework for rapid prototyping of magnetic resonance imaging sequences. Find ODIN at: http://od1n.sourceforge.net

Rating: 4.3. From 9 votes.
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Posted in Medical Sciences | Leave a comment

Wise2

Wise2 is package that is focused on comparing DNA sequences at the level of its conceptual translation, regardless of sequencing error and introns. Find Wise2 at: http://www.sanger.ac.uk/Software/Wise2/

Rating: 4.3. From 4 votes.
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Posted in Bioinformatics | Leave a comment